Archives for 2013 | Macs in Chemistry
There is an interesting post on
on the use of
to solve chemistry homework problems. I have to say I continue to be impressed by Wolfram Alpha, the breadth and depth of science that is covered is amazing.
For science apps for iOS have a look at the .
I was just reading the end of year newsletter from [Molsoft] and I came across this interesting snippet.
MolSoft is excited to announce that Anaglyph 3D is now available to use in ICM and .
Sure enough the update on Dec 24th has this in the release notes.
Anaglyph stereo mode is added. (Set 'Stereo Type' to 'Anaglyph' in Tools menu) Any red-cyan 3D glasses will work in this mode.
There are a number of suitable glasses on Amazon
I think this is the first app to enable this sort of stereo viewing and it just underlines the strides that mobile platforms are making in scientific computing.
For science apps for iOS have a look at the .
Ever had problems with an unusually formatted PDB file?
is a file conversion tool for PDB files that might interest you. It was created by Tomasz Wo?niak
at the Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences
PDB format is the most commonly used by various programs to define three-dimensional structure of biomolecules. Those programs however, often use different versions of this format. Therefore, it is often necessary to write own re-formatting scripts or change files manually, which makes PDB files less convenient to use. There are only few tools allowing to change one or two versions of PDB format into another and no comprehensive approach for unifying PDB format was developed. Here we present an open-source, Python-based tool PDBinout for processing and conversion of various versions of PDB file format for biostructural applications. Moreover, PDBinout allows to create one&s own PDB versions.
also includes a tutorial.
Reference Wo?niak T. and Adamiak R.W. (2013) Personalization of structural PDB files, Acta Biochimica Polonica 60, Paper in Press
Registered Apple Developers can watch full sessions from the iOS 7 Tech Talks to&get in-depth guidance on developing for iOS 7. Discover how to create innovative, flexible, and intuitive apps that integrate the latest Apple technologies.
For science apps for iOS have a look at the .
The hugely popular reference management application Papers has just been updated.
has a new cleaner interface and a host of new features.
The mobile app
has also been updated.
I noticed that
a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. is now available on
expanding the list of available Computational Chemistry packages. The following packages are also available.
CP2K, LAMMPS, GAMESS, GROMACS
I&ve added a minor update to the
One of the issues with the original script that the mol file contains in its first line the incorrect title of the file (it appears to be the name of the document template).
When you just launched your ChemDraw application, or created a new document, the title would be &Untitled **&, such as "Untitled ACS Document 1996-1". When you save it as Mol file, its header block will inherit the current document title "Untitled ACS Document 1996-2&.
Untitled ACS Document 1996-2
It would be better to have the molfile title the same as the file name the user enters in the dialog box, one way to achieve this is to &edit& the file and then save again to the same file name. We can do this by adding a line to clean up the structure and then saving.
save first document in (molAttachment) as "MDL Molfile&
--This is to ensure the title of the mol file is set correctly
do menu item "Clean Up Structure" of menu "Structure"
save first document in (molAttachment) as "MDL Molfile"
close first document saving no
If you now look at the mol file in a text editor you can see the title is set more appropriately.
Mol file1.mol
When I logged in the morning the first message I noticed announced the eagerly awaited MacPro was
with delivery on December 30th, within an hour or so that delivery time had changed to January, when I check now the delivery has moved to February. Well at least it is free delivery.
It will be interesting to see how long it takes Apple to sort out supply and demand.
It has been just over a month since I set up the
database and I thought it would be good to have a look at how things were going. The aim of the database was to enable scientists to be able to search for scientific apps for iOS.
It took a lot of work to compile all the information so I&m delighted to see that it has been accessed nearly 1500 times with visitors from all over the world. A fair number of people have been
for their favourite application and it perhaps not surprising that the chemical drawing applications, ,
are all in the top 5. The other apps picking up votes are popular scientific search and computation tool
and the award winning reference management app , together with
an app that allows you to search a local copy of the 1.2 million record ChEMBL database, an app that really demonstrates the computing power now available in a hand-held device.
I will of course continue to update the database but since finding science apps on the iTunes Store can be a challenge I&d be delighted to hear about any that I have missed.
I thought I would highlight a recent publication I read
in Journal of Cheminformatics &Molecule database framework: a framework for creating database applications with chemical structure search capability& Journal of Cheminformatics &.
From the abstract
Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:Chemical structure searches combined with property searches. Support for multi-component compounds (mixtures)
mport and export of SD-files. Optional security (authorization). For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files.
While not a drag and drop solution it provides a means to create your own personal chemically searchable database.
Molecule Database Framework is available for download on the projects web page on bitbucket: .
OpenEye have just announced the release of& a database of high quality experimental pKa determinations. The ionisation state of a drug molecule can have profound effects on affinity, dissolution, absorption, distribution, metabolism and off-target activity. The ability to predict pKa is often compromised by the lack of relevant experimental data, pKa Prospector is intended to address that issue.
The built-in experimental pKa database was compiled by Tony Slater of pKaData Limited from a collection of IUPAC sources. Each measurement has been individually verified, curated, and assigned a metric of quality. There are more than 30,000 experiments across 12,000 molecules represented. The database is particularly relevant for medicinal chemistry due to the strong preponderance of room temperature aqueous measurements, the many molecules with multiple experimental records, and the presence of over three hundred different heterocycles.
It is also possible to add additional experimental results and have them integrated into the application thus expanding the chemical space covered. The search uses rooted maximum common substructure (MCS) with "electronically-aware" scoring, alternatively it can be searched by similarity or substructure. Ionizable groups are automatically identified and highlighted.
A number of publishers are seeking to add extra value to publications by including access to chemical structure information to aid searching and indexing. More details are included in this comment from Elsevier.
Elsevier would like to enrich online articles by visualising and providing details of chemical structures you define as the main chemical compounds described in your article. For this purpose, mol files of the key compounds can be uploaded in EES. Please use your preferred drawing tool to export chemical structures as mol files and ensure that they are well defined and do not contain aromtic bonds, R-Groups or other variables.
Submitted mol files will be available for downloading from your online article on ScienceDirect. Furthermore, Elsevier will generate InChI keys from the mol files and include them in the online article, which increase the online searchability of your article e.g. in Google. InChI keys will also be used to link the article to additional data in Reaxys.
Since you need to export each structure as an individual file this will become somewhat tedious, fortunately
has written an
that greatly helps the process for ChemBioDraw users
Now updated.
I&ve just added
I thinking of upgrading my 5 year old MacBook Pro, in particular I was thinking of installing a solid state drive. I know I can replace the old hard drive but I was wondering if might be possible to replace the DVD drive which I actually never used. Has anyone any experience of this?
Originally Theodore Gray produced a beautiful coffee table book The Elements: A Visual Exploration of Every Known Atom in the Universe, this was later converted into an iPad app
which gave access to more dynamic information than could be achieved with a hard copy book. Now the developers have gone one step further and created
a periodic table with video explorations of the properties of elements. Some of the videos look like they have been rescued from old research labs so this is probably your only opportunity to see them in action.
Whilst there are a number of desktop applications that allow for the creation or editing of 3-dimensional chemical structures there are not as far as I am aware any tools for editing the 3D structure within a web page. CH5M3D uses a combination of HTML5 and javascript to interactively draw and edit 3-dimensional structures of small molecules.
The details are described in a recent publication Journal of Cheminformatics
, it can be downloaded from , and you can try it out on the .
The latest update to the increasingly popular chemical drawing package
has just been released. ChemDoodle 6 is the latest update from iChemLabs and once again it supports Mac, Linux and Windows and works with most document creation packages. This is apparently a free upgrade for those who recently purchased ChemDoodle 5.
I plan to write a review of ChemDoodle 6 when I have time but looking at the release notes this looks to be a substantial update.
New features in ChemDoodle 6:
IUPAC naming with over 20 options!
Carbon nanotube and prism builders. Both zigzag and armchair nanotubes can be built. These tools quickly produce 3D geometries.
Auto updating labels can now be attached to molecules, so they will update with IUPAC names, molecular formulas and more.
Mac OS X Quick Look plugin. Easily preview all your chemical files in Finder just by pressing the space key.
More Windows support, including a more powerful tool for supporting Windows filetype associations with the option to unassign types, support for the MDLCT and MDLSK clipboard formats for copying and pasting between a wider array of chemical applications, and greatly improved OLE support to allow for double-clicking to edit structures.
More glassware, including a new organized glassware window. You can now also remove liquid from the templates.
Significantly improved graphics. Graphics in ChemDoodle were already very good, but we took a look at all the graphics at very high scales and resolutions. We have made sure to focus on all the little details. Bond join edge cases have been improved. Hashes are now auto centered, making recessed bonds and dashed bonds look much nicer. Other bond types have been scrutinized for the best aesthetics. Convex hull algorithms have been built for better placement of bonds around labels. Cis double bonds will now prefer the inside edge. Circles over charges now only surround the number. Aromatic ring circles now meld to the shape of aromatic circles. Arrows look nicer. You won't find better graphics in any other application.
3D coordinate generation.
A new 180& chain angle clean option for easily creating Lewis structures and figures with 90& angles.
Complex embedded ring systems (like corannulene) now clean very well in 2D.
Added resolution controls to the Elemental Analysis widget.
Meso stereochemistry support.
An advanced formatted text system for the system clipboard. You can now copy and paste your molecular formulas, IUPAC names and others into word processing applications with formatting intact.
Many other minor, but useful features: option for the delete key to decrement bonds, nominal mass counter, improvements to the TLC Plate widget, improvements to arc placement previews, alt and shift now modify attribute placement just like placing bonds, improved file chooser previews for data files, more templates for the Templates widget, and more.
Squashing of dozens of bugs.
Remember also that there are also .
ChemDoodle Mobile, the mobile companion to ChemDoodle, is provided for free to ChemDoodle desktop customers. ChemDoodle Mobile is available for both iOS (iPod Touch/iPhone/iPad) and Android devices. You can transfer structures between ChemDoodle desktop and ChemDoodle Mobile, to take with you into the lab
A couple of applications from
have been updated.
is a content management system providing crowd sourced information on a range of tropical and neglected diseases. The ODDT app is free. It can be used anonymously to browse topics.
Submission of content requires the user's Twitter account to be enabled and made available to the app.
allows specially crafted molecular glyphs to be snapped by the device camera, which direct the app to chemical data: molecules, reactions and collections. This update fixes a bug that could cause the app to crash.
update includes Sketcher improvements: crayon gestures for ad traversal gesture for grow and a "band-aid" feature for fixing badly drawn chain bonds.
There is now a searchable
I&ve added
to the alphabetical listing of applications.
CPMD&is an&ab initio&electronic structure and molecular dynamics (MD) program using a plane wave/pseudopotential implementation of density functional theory (DFT). It is mainly targeted at Car-Parrinello MD simulations, but also supports geometry optimizations, Born-Oppenheimer MD, path integral MD, response functions, QM/MM, excited states and calculation of some electronic properties.
Full installation instructions are available on the website together with the user manual and examples.
The examples can run effectively on an Intel Core i5 (2.53 GHz, OS/X) with 4 GB of available memory (most of tests require ca. 1GB, few more). Nonetheless, references have been generated on an IBM Blade power7 (with 8 mpi tasks and 1 OMP task per CPMD run) with 64 GB of available memory. Estimates of the execution time and memory requirements will be given based on this more performant setup.
CPMD capabilities
Works with norm conserving or ultrasoft pseudopotentials
LDA, LSD and the most popular gradien free energy density functional implementation
Isolated systems and system with periodic k-points
Molecular and crystal symmetry
Wavefunction optimization: direct minimization and diagonalization
Geometry optimization: local optimization and simulated annealing
Molecular dynamics: constant energy, constant temperature and constant pressure
Path integral MD
Response functions
Excited states
Many electronic properties
Time-dependent DFT (excitations, molecular dynamics in excited states)
Coarse-grained non-Markovian metadynamics
CPMD is free for non-profit organisations.
I&ve just added
to the page of
Graph-R is an application used to create 3-dimensional contours, contour lines, wire frames, and scatter diagrams from numeric data files(CSV files). Graph setting is easy. The perspective direction can be freely changed using your mouse. Graph that are created can be saved as PNG or JPEG files.
This software requires Mac OSX 10.8 or later.
is now available, the focus of this release is to extend the capabilities available via the standalone PYTHON interface to 3D-QSAR, which was introduced in SYBYL-X 2.1 earlier this year. The PYTHON API allows 3D-QSAR models (CoMFA, CoMSIA, and Topomer CoMFA) to be created and used for predictions outside of SYBYL-X.
Hologram QSAR (HQSAR) is a now available via Python. &HQSAR has been successfully applied to generate predictive global QSAR models for on- and off-target effects and models for important ADME the HQSAR method employs 2D-substructural counts as descriptors.
Similarity computations and similarity searches (UNITY 2D fingerprints) are now accessible via Python to support various workflows, such as lead expansion, lead hopping, and cluster analysis.
extensively on my websites, &Markdown& is two things: (1) a plain te and (2) a software tool, written in Perl, that converts the plain text formatting to HTML allowing you to build HTML documents in an easily readable form. As the use of Markdown has increased in popularity there are now a wide choice of Markdown editors available for MacOSX and recently iOS so i&ve updated the.
Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. Given that this seems to be such a major upgrade I thought I&d set up a spare machine to test applications before I update my main machine.
The update went smoothly albeit with an overnight download of the 5.5 GB file.
The update removes both
and java so both of these need to be reinstalled, if you forget you will be prompted to download the first time you try to use them.
No issues with cursory testing,
users or vendors provided feedback
ChemDoodle
ChemSpotlight
Cresset software (forge, torch, spark) (no reported issues)
FTranProjectBuilder
ICM-Homology
ICM-Chemist
iNMR (No reported issues)
OpenEye (Command line tools
OMEGA 2.5.1 (OSX 10.8 version), FILTER 2.5.1 (10.8), ROCS 3.2.0 (10.8), SZMAP 1.2.0 (10.8), EON 2.2.0 (10.8), QUACPAC 1.6.3 (10.8), SZYBKI 1.8.0 (10.8), FLYNN 2.3.0 (10.8), The Python and Java toolkits work fine. The C++ toolkit can be made to work if some of the compiler flags are changed. Please email
for more details. For the OpenEye GUI applications, vROCS 3.2.0 (OSX 10.8 version) works fine, for other apps see below
R latest version R 3.0.2 ("Frisbee Sailing")
Reference Tracker
Some issues :-(
MOE install
I downloaded the latest update as a zip file and unarchived it. When I double click on the installer I got a message that it was broken or corrupted.
This seems be an issue with the Mac OSX Gatekeeper,
Open Apple menu, then go to System Preferences -> Security & Privacy -> General tab.
In the option list of "Allow Applications downloaded from", select "Anywhere".
Then installs OK.
Once installed MOE seems to run fine.
CCDC Software
Mac OSX 10.9 causes most CCDC software to fail - there are
now have patches available that address this issue.
For enCIFer 1.4:
For the 2013 CSD System go to:
For standalone Mercury 3.1 or 3.1.1 go to:
These updates should only be applied on Mac OSX 10.9. NB One reader reported issues with the update.
ChemBioDraw
Chemdraw 13 files pasted into Keynote 6 cannot be copied and pasted back into ChemDraw. In addition, if you open old Keynote files in Keynote 6 all the ChemDraw cannot be copied and pasted. It pastes into Chemdraw as a picture with an all black background.
In Mac OS 10.9 with Keynote 5 - round trip editing still continues to work.
According to the
there are issues with copy/paste in CD 13 to Office 2011 for Mac. Any CD structures that are pasted into PPT or Word cannot be opened or edited with CD.
EndNote X7
We have tested EndNote X7 with&Mac OS X 10.9 Mavericks to determine compatibility. We have found some minor issues and are working on a free update patch to be released in the next few weeks.
EndNote X6
EndNote&X6&is&not officially compatible with Mac OS X 10.9 Mavericks. We are testing EndNote X6&with Mac OS X 10.9 Mavericks to determine informal compatibility and will report any exceptions found on this page.
EndNote X5 and earlier
Due to major compatibility issues, it is not recommend to&attempt to use&EndNote&X5 or earlier on OS X 10.9.
When attempting to launch EndNote X5 or earlier, a warning message comes up that will include "unable to load ....ENCore.Bundle". EndNote X5 and earlier will fail to launch after receiving this message. There are no known workarounds for this issue besides moving to a more recent version of EndNote or restoring your computer& (using a Time Machine Backup for example) to a previous version of Mac OS X.
OpenEye Command line tools that require setting the OE_ARCH environment variable (FRED 3.0.1 (OSX 10.7 version), HYBRID 3.0.1 (10.7), POSIT 1.0.3 (10.7), LEXICHEM 2.1.0 (10.6), BROOD 2.0.0 (10.5)
export OE_ARCH=osx-10.9-x64:osx-10.8-x64:osx-10.7-x64:osx-10.6-x64:osx-10.5-x86
For the OpenEye GUI applications, vROCS 3.2.0 (OSX 10.8 version) works without any issues. VIDA requires the OE_ARCH modification shown above but also needs the following additional fixes:
sudo mkdir -p /Applications/OpenEye/arch/osx-10.6-x64/vida/4.2.1/bin/QtCore.framework/Versions/4
sudo ln -s /Applications/OpenEye/arch/osx-10.6-x64/vida/4.2.1/bin/QtCore /Applications/OpenEye/arch/osx-10.6-x64/vida/4.2.1/bin/QtCore.framework/Versions/4/QtCore
Unfortunately, the current vBROOD, AFITT, and MAKE_RECEPTOR GUIs do not work on Mavericks. We are actively investigating these issues.
Using Aabel v3 on Mavericks is not recommended due to cosmetic glitches such as misalignment of graphic viewer icons on the Mavericks buttons. Mavericks will be supported in the next major version of Aabel
Papers2 update about to be released
If I hear of anything, I&ll update this page.
have been updated, the release notes don&t give much information on the updates other than Redesigned for iOS7 and bug fixes.
The use of mobile devices in teaching has offered new opportunities and a recent presentation by Layne Morsch illustrates this quite nicely. . The page has a couple of embedded videos that give more details.
The other feature that is now becoming mainstream is the
and since Chem3D can export in .stl format it is not surprising people have started to experiment with creating 3D models of molecules, there is a brief video , unfortunately it is a loop of the printing process so don&t expect to see the final product. CambridgeSoft have also produced their own videos of these
A couple of apps have been updated recently
the world's definitive source for instant expert knowledge and computation.
allows specially crafted molecular glyphs to be snapped by the device camera, which direct the app to chemical data: molecules, reactions and collections
There is now a
I just saw this message from Shane Stanley
As some of you have probably found already, Xcode does not recognize AppleScript's new interleaved syntax when used for action handlers -- you cannot make connections to them from controls. The workaround is to keep using the underscore syntax for action handlers until the problem is resolved. That's not ideal if you use an external editor, though. FYI, I've just released a new version (3.0.7) of
for Mavericks to deal with this issue. There is a new preference setting in Preferences -> Other. When checked, every time you save a .applescript file, any single-argument handlers will be changed to use old-style underscore syntax. (The new syntax will appear in Xcode and in the saved file, while the new syntax will still appear in Explorer.)
has been updated this contains X11 2.7.5 the first release supported on Mavericks. Full details are available
The XQuartz project is an open-source effort to develop a version of the X.Org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.
There was a blog entry on
about a bug in ChemDraw. Actually this has been known for a while (and present in previous versions) but it seems it still has not been fixed in the latest version of ChemBioDraw 13 on the Mac. As you can see in the image below including explicit hydrogens in your structure significantly impacts the calculated LogP. Whilst people don&t often add explicit atoms to phenyl rings, (expect perhaps in SAR studies) they often add them to heteroatoms.
At the moment there is no bug fix and no date set for a fix to any version of ChemBioDraw, the only approach is to avoid adding explicit hydrogens to structures if you want to calculate LogP. I&ve looked at a number of other applications and there seem to be no issues with ChemDoodle, Elemental, Marvin or OpenBabel.
I just got a message about an update to
a very popular and powerful application from VVimaging, Inc rich in graphic editing, creation and programming to facilitate the visualization of information. It has a excellent complement of 2D and 3D graph features, a full-fledged user interface and is programmable. Paste data into table editors, write scripts to generate data, load a Xcode plugin you write for data generation and to retrieve data from external sources. Also supports dynamic graphs.
site expands I&ve started to add other resources in addition to the applications. There are now a couple of useful additions for
if you are looking for a training course, a plotting library or a chemistry toolkit.
I&d be delighted to add any more useful resources.
provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.
An interesting article on plans to build a supercomputer based on cellphone chips. It seems the low power consumption of ARM processors make construction of a supercomputer based on those chips an attractive proposition.
His project is part of a larger movement towards this new breed of low-power chips. As Ramirez builds an ARM supercomputer in Spain, web giants such as Facebook and Amazon are exploring the use of these low-power chips in the servers that run their massive online services.
Finding scientific applications for your iPhone to iPad has always been a little hit and miss since there is no &science& category on the iTunes store. To help out I created a page listing applications that I knew about, unfortunately as the number of applications increased the page became unmanageable. In addition an alphabetical listing is not the most useful way to search through them.
I&ve now transferred all the information to a database that can be searched via a web interface.
The site is available at , I&ve started to categorise applications to aid navigation but I&d be interested to hear of any suggestions. Currently there are over 200 entries covering an extensive area of science, if I&ve missed any please let me know and I&ll add them.
In the news section I&ve added links to publications and presentations that might be interesting.
I&d encourage to have a look around and I&d be interested to hear any comments or suggestions.
OpenEye have just released an update to SZYBKI with a host of new features. SZYBKI is used to optimise the three dimensional structure of molecules prior to their use in other programs. SZYBKI also refines portions of a protein structure and optimize ligands within a protein active site, making it useful in conjunction with docking programs.
New utility program called FreeForm is available for Szybki users. It provides two distinct functionalities: evaluation of the solvation free energy of the input molecules and free energies of solution conformations. Please Note: FreeForm is not available under 32-bit Windows because of the high memory requirements of this application.
A new forcefield for protein-ligand interations is available upon selecting a new option -ff followed by AmberMMFF94 or AmberMMFF94S. It is a combination of MMFF94 (or MMFF94S) with Amber. In this combined force field, MMFF94 (or MMFF94S) is used to describe the intramolecular interactions of the ligand and the Amber force field is used for the VdW and Coulomb interactions between ligand and protein. Currently, this force field can be used only for ligands inside rigid proteins.
Entropy estimation based on analytical MMFF Hessian is extended for ligands bound in a rigid protein using the option -entropy.
Constraining torsion potential in the form: , where
is the user specified force constant and
is the reference torsion dihedral angle is available with the use of the input flag -tor_constr.
New option -optMethod is introduced for optimization method selection. The possible choices of optimizers type are BFGS, conjugate gradient, steepest descent and mixtures of steepest descent preoptimization followed by BFGS of conjugent gradient. Option -conj is no longer supported.
Optimization of molecular systems with large number of degrees of freedom (>= 500) is by default done with the conjugate gradient method unless specifically requested with the option -optMethod.
New option -optGeometry is introduced for selection of coordinate system to be used during optimization. It replaces no longer supported options -optcart, -opttorsions, -solid and -noopt. It can be also used to optimize hydrogen atoms positions only, instead of using for that purpose -fixsmarts.
Molecules from the input file which failed during processing are by default written to the separate molecular file. See the description of new option -keepFailures.
Starting from this release flags -fixsmarts and -harmsmarts are followed by the name of the text file containing a single line with a SMARTS pattern used to fix or constrain atoms. Input of SMARTS strings on the command line for those flags are not used anymore because some SMARTS strings may contain special characters which may be interpreted incorrectly on some platforms.
The popular reference management package ) has been recently updated and fully supports Mavericks.
Improved ISBN lookup.
Improved article search.
Fixed a bug where incomplete reference styles could be shared to the cloud.
Fixed a bug where ISBN lookup results could be imported with missing data.
Fixed a bug where open link buttons in documents could reposition incorrectly when the document window was resized.
Fixed a bug that could cause Reference Tracker to crash on startup on OS X 10.7.
Fixed tabbing between fields in the Publication Search sheet.
I also note that there is a special offer at the moment
Reference Tracker is available at a special 30 % discounted price until 30 November 2013!
There is a
ChemAxon have released a new update to Marvin.
MarvinSketch GUI
MSketchPane setPiece(Molecule) method did not work, it set the molecule on the canvas instead of putting it on the cursor.
Import/Export
CXSMILES/CXSMARTS
CXSMARTS containing valence property information was recognized and read as SMARTS.
Some reaction was read as R-definition from SKC format.
I just learned of an interesting site that is currently under construction.
has a number of tutorials on how to use the new speech recognition features in automator actions.
Well worth spending a few minutes watching the video tutorials.
One of the big changes with Mavericks is the enhanced security and this has an impact on all developers even those who write a &simple& applescript to avoid a tedious or repetitive series of actions.
Developers have often relied upon AppleScript&s ability to control the user-interface, to provide an automation solution when no direct scripting support of an application or process was available. While this valued ability continues to be fully supported in Mavericks, the enhanced security focus of the new OS requires a few changes in how scripters access and apply the Accessibility frameworks.
There is a really comprehensive discussion of
over on Mac OS X Automation. Well worth a read.
I&ve just updated the listing of
and I thought I&d highlight one application. The page I have on
is consistently one of the top accessed Blog entries. I&m sure one of the reasons for this popularity is
the only Mac-native Fortran development environment (IDE) it works with the gfortran, g95, ifort, Absoft Pro Fortran, NAG nagfor and PGI pgfortran compilers. Since I mentioned it last FTranProjectbuilder has been updated six more times, in April, May, July, August and October with new features like the ability to build static libraries, trackpad interaction and compiler errors now being marked in the source code. Full details are in the
on the Nocturnal Aviation Software website , and yes, all of the tools, including FTranProjectbuilder
are compatible with 10.6.8+, and run fine on 10.9 Mavericks.&
Fortran still has a significant user base in the scientific community where the speed, portability, array handling and access to shared memory make it a very powerful option.
There is a nice comparison of programming languages from the viewpoint of scientists
I&ve just been sent a link to , this allows the user to explore DNA-seq and RNA-seq pile-up and coverage data in an intuitive manner. Whether viewing one file or many, an integrated approach is taken to exploring your data in the context of rich annotation tracks.
Features include:
Zooming and navigation controls that are natural as they mimic panning and scrolling actions you are familiar with.
Coverage and pile-up views with different modes to highlight mismatches and look for strand bias.
Deep, stable stacking algorithms to look at all reads in a pile-up zoom, not just the first 10 or 20.
Context-sensitive information by clicking on any feature. See allele frequencies in control databases, functional predictions of a non-synonymous variants, exon positions of genes, or even details of a single sequenced read.
A dynamic labeling system which gives optimal detail on annotation features without cluttering the view.
The ability to automatically index and compute coverage data on BAM or VCF files in the background.
GenomeBrowse integrates with the powerful Golden Helix SNP & Variation Suite (SVS) analysis platform. SVS can be used to build custom annotations and perform variant analysis, while GenomeBrowse can visualize findings and validate the evidence for putative variants.
The free univariate data modeling package .
Regress+ offers:-
Plain textfile input
Equations, with or without uncertainties (weights)
Distributions, continuous or discrete data
Discrete data grouped or ungrouped
Datasets up to 4,294,967,295 points (minimum 7)
Up to 10 parameters
User-selected optimization criterion (where appropriate)
Least squares
Minimum average abs(residual)
Maximum likelihood
Minimum K-S statistic
Minimum chi-square statistic
Full, dated Report (textfile)
Robust goodness-of-fit testing for distributions
Tunable precision
[Optional] State-of-the-art (BCa) central confidence intervals (90, 95 and 99 percent)
Tunable precision
High-quality (PDF, PNG) plots with one keystroke!
X/Y plot, with or without error bars
Probability plot for goodness-of-fit (see above)
[Optional] Logarithmic axes (when appropriate)
Editable axis labels
Automatic tick marks/labels (see above)
[Optional] Predictions for unobserved values or percentiles
With confidence intervals if desired
[Optional] Constant parameter(s)
21 Built-in Equations
Plus user-defined model
[Optional] Test residuals for systematic error
[Optional] List data with fitted estimates and residuals
[Optional] Simulated-annealing mode for initial parameter estimates
59 Built-in Distributions
9 continuous, symmetric
27 continuous, skewed
11 continuous mixtures
6 discrete
6 discrete mixtures
[Optional] Creation of synthetic samples
No hidden assumptions anywhere
No approximations, apart from those common to sampling and bootstrapping generally
No data transformations of any kind
Extensive documentation
There is comprehensive listing of .
I&ve been looking at the rate of
currently it stands at 13-15% which is quite impressive. Interestingly most of the early adopters seems to be those running Mountain Lion, the numbers using Lion and Snow Leopard seem to be pretty much unchanged.
I&ve also updated the post regarding , if anyone has any more comments I&ll continue to update the page.
Myriad Communications has released its successor to AppleScriptObjC Explorer, available immediately. The new editor takes advantage of the improvements to AppleScript in the latest release of OS X, which make access to Objective-C frameworks from AppleScript easier than ever.
"The changes to AppleScript in Mavericks have largely flown under everyone's radar, but script libraries open lots of doors for scripters," says the application's developer, Shane Stanley. "Bridging between AppleScript and Objective-C code has become much easier. This sets a new direction for expanding AppleScript's abilities."
ASObjC Explorer for Mavericks is designed to make developing AppleScriptObjC-based script libraries simple, with everything you need in one window. It features customised syntax formatting to take advantage of the ne intelligent code-completion and shortcuts to take the tedium
logging, stepping and breakpoints and a built-in simplified scripting-definition editor for adding English-like terminology.
It also makes an ideal external editor for AppleScriptObjC-based Xcode projects in Mavericks
ASObjC Explorer for Mavericks can be downloaded from &>, and can be used free for 30 days. The purchase price is $US49.95.
For further inquiries, contact Shane Stanley at &>.
New features and improvements
MarvinSketch Dialog
'Zoom to scaffold' checkbox option has been added to the "Preferences>Save/Load" tab. Documentation
Structure Checker
External structure checker configuration file URL can be set via Java System Property.
Electron-flow arrow could not be drawn from the A-B bond to the incipient A-C bond of an A-B-C structure. Forum
Import/Export
MolInputStream and MolImporter could have different format options.
MolImporter did not close its inputstream when an exception was thrown in the constructor.
MOL, SDF, RXN, RDF
Molecule type property was allowed in SDF, CSSDF export.
The coordinates of the sequence residue imported from SCSR MOL files were wrong if the residue had three attachment point.
Color and text format of atom label is exported to CDX and imported from CDX and CDXML. Forum
Graphical brackets were not imported from CDX files.
Gaussian Z-matrix input format
Command line, title line, and extra input properties were not exported to Gaussian Z-matrix input format. Forum
Cleaning of position variation bonds could create overlapping bonds.
Cleaning of bridged systems could result in overlapping atoms. Forum
Calculations
Topology Analysis
Missing method has been added: TopologyAnalyserPlugin.getFsp3(). API Documentation
New logD training documentation has been added. Documentation
Structure Checker
Fixer options in MarvinSketch are updated with newly defined settings.
External checkers can be loaded from JAR file in case the JAR file contains a space.
have just announced the release of the latest update of MOE (Molecular Operating Environment).
General Updates
Extended H&ckel Theory for Pharmacophore Discovery
Apply EHT strengths to identify and discover weak and strong interactions
Annotate non-standard interactions: halogen and CH bond donors
Score pharmacophore hits using sum of interaction energies
de novo Loop and Linker Modeler
Search and browse for de novo and knowledge-based loop candidates
Generate multiple loop conformations and score loop-loop interactions & Investigate linkers for fusion proteins and dual variable domains
Protein Alignments and Superpositions
Superpose protein structures independent of sequence
Apply new threading methodology for sequence to structure alignments
Align sequences and superpose structures using STOVCA criteria
Core System Enhancements (with 64-bit support) The default versions of MOE for Linux, Windows, and Mac OSX are now all 64-bit. The current release also includes 32-bit versions for each architecture.
Create additional data grouping level in System Manager
Handle large number of protein:ligand complexes in real-time
Colour database viewer text and cells by data values for enhanced analysis, Empty cells can be specially colored
Interface to Mogul from CCDC
Access a knowledge-based library of small molecule crystallographic data
Visualize histograms and statistics fo rbond angles, dihedrals and torsions & Ensure ligand conformation is consistent with the CSD
Solvent Analysis using 3D-RISM Enhancements
Calculate water densities on full protein or protein:protein interface
Accurate placement and stability prediction of water sites
Use3 D-RISM densities to validate water position in crystal structures
chEMBL Library. MOE's SD Pipeline Command Tools were used to generate fragments from Release 14 of the ChEMBL database of bioactive drug-like small molecules. The resulting database of conformations, chemblr14_frag.mdb, for approximately 830,000 fragments, suitable for Scaffold Replacement or combinatorial chemistry methodologies
Mac OS X Enhancements.
OS X Dock Icon Enhancements. A new Dock menu, accessed by right-clicking (or control-clicking) the MOE Dock icon, allows for standard Mac OS X operations & Hide, Show, and Quit & across all open iterations of MOE. The Dock Menu also contains menu items in order for users to view the About panel bundled in MOE, as well as access the Preferences panel. Additionally, the Dock indicator light under the MOE Dock icon remains persistent after having launched a new instance of MOE, until all opened MOE instances have been closed. Users continue to be able to drag and drop compatible MOE documents (i.e. .pdb, .svl, etc.) onto the Desktop and/or Dock icons for direct opening in MOE.
New Preferences Menu. A new Preferences panel allows for certain parameters to be set and/or changed graphically. These parameters include the defaults key and path to MOE, the current configuration of MOE (32- or 64-bit, or Auto-select), as well as a selection of common command line tags, with a custom section for inputting other command line options.
Output Continuity. stdout and stderr received from MOE have been standardized to be displayed in a native panel in a scrollable text box.
from Nano3D Biosciences. This application helps organize and analyze data from experiments. It take manual photos and automatic shooting for multiple images and time lapse movies, and stores them in albums for easy access later
There are updates to both and ) for iPad. There is little information available about the update to version 2.0 other than &bug fixes& and the apps have been redesigned for iOS7 and now have a minimum requirement for IOS7.0 or later.
contains a listing of science apes for iOS.
A reader just pointed out that the support site for a couple of the items on the is no longer available.
The Amino Acid Table widget
The Genetic Code widget
The Nucleic Acid Nomenclature widget
The ProtParam widget
Whilst the widgets are still available from a number of download sites the support site "" domain is labelled as for sale.
I just noticed that there is an update to R on the
This binary distribution of R and the GUI supports 64-bit Intel based Macs on Mac OS X 10.6 (Leopard) or higher.
Since R 3.0.0 the binary is a single-arch build and contains only the x86_64 (64-bit Intel) architecture. PowerPC Macs and 32-bit Macs are only supported by building from sources or by older binary R versions. The default package type is "mac.binary" and the binary repository layout has changed accordingly.
There is a .
is a free open access site of annotated models and chemical data. OCHEM contains 1831772 experimental records for about 477 properties collected from 12457 sources you are free to upload your own data and also build predictive models using existing or your own data.
There are also a number of already built models that the public can access, these include
CYP1A2 inhibition
LogP and Solubility
You can run predictions on OCHEM using simple REST-like web services,submit tasks to the various models and then retrieve the resulting prediction.
If you want to automate a process but don&t want to learn Applescript then
may be of interest.
Repeater provides a much needed and very convenient platform for recording repetitive actions without having to learn and understand Automator or AppleScript, which are well beyond most user's abilities. Moreover, not all apps can be scripted at all, but Repeater can help you anyway.
Furthermore, you can integrate Repeater with popular scripting languages to dramatically improve their possibilities.
Repeater is a tool specially designed for recording and playback user actions such as mouse movements and clicks, standard and hardware keystrokes, vertical and horizontal scrolling & zooming. It is also capable of storing information about currently running applications to launch them on playback.
There are also some scripting capabilities for more advanced use. Looks like it could be useful for giving demonstrations.
I&ve recently been sent details of , an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It is released under BSD/3-clause license and is supported under Mac OS X: GNU/g++, LLVM/Clang (3.0+).
Andreas D&ring, David Weese, Tobias Rausch and Knut Reinert.&SeqAn an efficient, generic C++ library for sequence analysis.&BMC Bioinformatics, 9:11, 2008.
I&m hearing more and more concerns about security concerns with regard to mobile devices. I guess this was to be expected as more people have smart phones and tablets start to replace laptops. It seems Google's executive chairman Eric Schmidt drew laughter when discussing security on the Android platform, .
Schmidt said in the distant future there would be an assumption that nothing is secure and that security will be devised on a per app basis for each user.
I&m not sure whether many people would find that situation very helpful. His view is perhaps a consequence of a recent study issued by the Department of Homeland Security (DHS) and the Federal Bureau of Investigation (FBI) suggesting . Of the malicious attacks documented in the study, 79 percent took place on an Android device and 19% on Symbian whilst Apple's iOS received just 0.7 percent of the recorded malware threats. One of the key sources of threats appear to be the installation of apps from insecure sites, so whilst the approval process for the Apple iTunes store occasionally causes complaints it also acts as a significant security barrier. Whilst the Google Android should have the same role it is perhaps worrying to find that recently . There have however now been reports of threats distributed via .
The Android trojan known as Stels began distributing via fake U.S. Internal Revenue Service-themed emails, using an Android crimeware kit to steal sensitive information from the device, and monetizing by making calls to premium numbers.
Apple does seem to be taking the security concerns seriously, the AppStore provides an initial check on apps, the new fingerprint authentication provides an extra level of device protections. In iOS7 we have
so that someone who&s got hold of your device can&t disable Find My
iPhone without knowing both your Apple ID and that Apple ID&s account password. The person with your lost device can&t erase data on the device, also if you designate your device as being lost it can&t be restored to reactivate it&the phone displays only a phone number and a custom message about contacting you.
Keeping the operating system up to date helps, and the
is very impressive.
Anyone involved in a drug discovery programme will be aware of the challenge presented by trying to visualise and explore structure-activity relationships (SAR), in particular visualising questions like :-
&What is the largest change that can be made whilst maintaining activity?&
Activity Miner from Cresset is a new tool designed to rapidly interrogate and decipher SAR in both Torch and Forge.
Activity Miner is intended to help identify key elements of the SAR by starting from a set of aligned molecules and then automatically comparing them to each other.
extensively on my websites, &Markdown& is two things: (1) a plain te and (2) a software tool, written in Perl, that converts the plain text formatting to HTML allowing you to build HTML documents in an easily readable form. I mainly use
and regard it as the &gold standard& but I keep an eye out for other markdown editors and wrote a , I&ve just been sent details of two more apps.
is a simple Markdown editor for the Mac. It is fast, extremely easy to use and gets out of your way. It offers full support for both regular Markdown syntax, GitHub flavoured markdown and YAML front matter.
is a previewer for Markdown files. Use it with your favourite text editor and it updates every time you save.
I&ve added them to the summary page.
has been updated
Added data input for 2D vector field presentation.
Added programmed and animated 2D vector field palette.
Updated script documentation for 2D vector field animation and programming.
Added a preference option to turn on the built-in network graphing server.
Added ability to display dynamic and programmed Graph Builder document results over the web.
Updated the manual to explain new features
There is a
OpenEye have just announced that the virtual screening tool
has been released.
Several noteworthy features have been added to this version including a -subrocs option that can drastically improve substructure alignments. Also included is an application rocs-report that uses our 2D depiction technology to make pdf reports of hitlists displayed with 2D similarity, shape and color overlaps, as well as property histograms. Substantial upgrades have been made to vROCS. An improved sketcher now highlights unspecified stereochemistry in atoms and bonds in query structures, and requires the user to correct any unspecified stereochemistry.
ROCS is available for .
I&ve just updated the ,
in particular I&ve included updates to the great tools provided by Satimage-Software. These include
a programming and working environment that you can use in a variety of situations. You may want to perform a scientific work, to handle cgi requests, to automate an intensive file processing task, to produce computed graphics, to edit XML files, to work with Unicode texts, to make GUI of your scripts,
the SmileLab license adds the data visualization features to Smile, the automation environment by Satimage-Software.
In SmileLab you can
extract data from files (default data formats supported: text, binary, FITS, XNF, ...),
perform data processing using commands provided with Smile or controlling external code
visualize your data in the most usual forms (curves, scatter plots, bar graphs, contour lines, color maps and vector fields in 2D, and 3D surfaces),
customize the interaction of the user with the plots (handling mouse clicks, contextual menus, keyboard events...) and create custom interfaces,
export your plot as a PDF file, as a bitmap picture (PNG, JPEG, TIFF, BMP, PSD) or as a QuickTime movie.
Simon McIntosh-Smith has just released a new OpenCL training course . It Includes a comprehensive set of exercises and solutions in C, C++ & Python.
There is a list of .
I was just looking at the
on the Mixpanel website. When I looked last night, iOS7 stood at 63% of users, iOS6 just over 32% with older versions of iOS below 4%. Given that iOS7 has only been available just over a week this is a remarkable adoption rate. Excellent news for all those
developers since it looks like will be able to focus their efforts on the latest version of the operating system,.
StarDrop was recently updated to version 5.4, this brings an update to the virtual library design module and scaffold based design, there have also been improvements to the plotting and data visualisation.
There are now
with three exciting new options.
Derek Nexus& - Knowledge based toxicity prediction
The new Derek Nexus module for StarDrop provides Lhasa Limited's world-leading technology for knowledge-based prediction of key toxicities. Using data from published and donated (unpublished) sources, Derek Nexus identifies structure-toxicity relationships that alert you to the potential for your compounds to cause toxicity. The Derek Nexus module provides predictions of the likelihood of a compound causing toxicity in over 40 endpoints, including mutagenicity, hepatotoxicity and cardiotoxicity.
BIOSTER& - A world of chemistry experience
BIOSTER is developed and updated in collaboration with Digital Chemistry and is available as an optional extension to StarDrop's Nova module. This combination enables you to quickly and easily search the comprehensive BIOSTER database to identify transformations that are relevant to your compounds. These can be automatically applied to generate novel structures with a high likelihood of biological activity and synthetic accessibility, prioritised against the property profile you require for your project.
BIOSTER brings the collective experience of the chemistry community to help you to discover new active analogues of your compounds based on the tried and tested principle of isosterism. The BIOSTER module contains a unique compilation of over 20,000 precedented bioisosteric transformations, manually curated from the literature by Dr Istv&n Ujv&ry, complete with references to the original publications in which they are described.
The renamed torch3D module, using Cresset&s unique Field technology to understand and apply 3D Structure Activity Relationship (SAR), has been updated to include the latest version of Cresset&s XED force field providing insight into compounds& 3D structures, biological activities and interactions.
These certainly significantly expand the potential utility of StarDrop, but note that these are not part of the standard install and may require additional licensing.
is a modern electronic structure program package written by F. Neese, with contributions from many current and former coworkers and several collaborating groups. The binaries of ORCA are available free of charge for academic users for a variety of platforms.
ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
New Features of Version 3.0:&
Improved efficiency in integral evaluation and digestion, thanks to Ed Valeev for the improved libint 2.0 library!
Improved parallelization, in particular for RI-DFT calculations.
The DLPNO-CCSD(T) near linear scaling local correlation method. It has led to the first CCSD(T) level calculation on an entire protein.
Explicitly correlated (F12) MP2 and coupled cluster methods using several approximations to boost the efficiency (They also work together with DKH/ZORA, COSMO etc.). Again many thanks for Ed Valeev for his countless contributions to this project.
Efficient analytic frequencies for RI-DFT, hybrid DFT, Hartree-Fock and MP2 (also featuring QM/MM Hessians, ECPs, DKH/ZORA, van der Waals corrections etc., COSX and RI approximations).
Interface to the large-scale DMRG program "BLOCK" developed by Garnet Chan and co-workers. it can be used together with the CASSCF module of ORCA.
The "HF-3c" method by Grimme and co-workers is a slightly parametrized Hartree-Fock variant that can be applied to very large systems and can achieve stunning accuracy.
Nonlocal van der Waals corrections have been implemented by the Grimme group
A range of modern functionals, including M06-2X, have been implemented by the Grimme group making use of the XCFun DFT library by Ulf Ekstrom.
Range corrected hybrid functionals have been implemented by the Grimme group
Coupled cluster densities and new coupled cluster methods like orbital optimized and Brueckner coupled cluster methods.
EOM-CCSD excitation energies for closed-shell systems.
MP2 electric and magnetic response properties (but no NMR yet).
A fully self consistent CASSCF method with spin-orbit coupling has been developed
The ROCIS module features a new approach to the calculation of complicated X-ray absorption spectra that are dominated by spin-orbit and multiplet effects
Natural transition orbital analysis for TD-DFT excited states.
Effective Hamiltonian (infinite order) extraction of EPR parameters from QDPT calculations using MRCI and CASSCF/NEVPT2.
The RIJCOSX-SCS-MP3 method.
Removal of near linear dependencies in the orbital basis set.
Improved overlap fitted COSX approximation.
Geometric counterpoise correction.
Finite nucleus for relativistic single point calculations.
Finite temperature SCF calculations and correct gradients.
Improved picture change theory for DKH magnetic property calculations.
Extended correlation energy extrapolation schemes making use of of LPNO methods.
Interface to NBO 6.0 and AIM.
Recently there has been an increased use of
format for data exchange.
JSON, or JavaScript Object Notation, is a text-based open standard designed for easy human-readable data interchange. It is derived from the JavaScript scripting language for representing simple data structures and associative arrays, called objects. Despite its relationship to JavaScript, it is language-independent, with parsers available for many languages including including C, C++, C#, Java, JavaScript, Perl, Python.
JSON is built on two structures
A collection of name/value pairs. In various languages, this is realised as an object, record, struct, dictionary, hash table, keyed list, or associative array.
An ordered list of values. In most languages, this is realised as an array, vector, list, or sequence.
JSON can be used to provide the results of a calculation via a web service or it could be used to provide the results of a database search, indeed the popular database
uses JSON-style document
storage. It can be regarded as less verbose alternative to XML.
I just noticed that there is now an Applescript parser for JSON,
Description.
is an agent which allows you to do useful things with JSON (JavaScript Object Notation) directly from AppleScript.
JSON Helper has no interface, and runs in the background waiting for AppleScripts to ask it to do something. JSON Helper is by far the easiest way to work with JSON in AppleScript.
JSON Helper lets you convert JSON directly into AppleScript records, and convert AppleScript records and list into JSON.
JSON Helper also makes it easy to parse the responses of many popular web services directly into AppleScript with convenience methods for fetching and parsing the responses from URLs.
I&ve added JSON Helper to the .
One of the new features in the latest version of MOE from
is the Listener. The MOE socket listener provides an alternative to MOE/web for executing functions remotely on a running instance of MOE.
The script will download the associated PDB structures from the , put them into a database then start the browser. It may take a few seconds to do this does rely on MOE having the right proxy settings to access the internet (use the Java console to set them). You can now transfer this to MOE and amend the display to highlight the ligand.
The MOEflexalign script takes the SMILES string of the selected row generates a 3D structure and does a one-shot flexalign between the ligand in the system in MOE, and the incoming ligand.
It is probably easier to see this in action, if it appears rather small click on the YouTube icon in the bottom right corner of the video.
&has been released:
New drawing and displaying features in MarvinSketch and MarvinView
Among others drawing peptid cycles and bridges is available now, and IUPAC numbers can be displayed in MarvinSketch and MarvinView
Better images to structures conversion in Document to Structure
Optical Structure Recognition tools CLiDE&and&Imago&can be used, in addition to OSRA
New Chinese Document to Structure feature
Chemical names in the flow of Chinese sentences are detected, without the spaces that separate words in English
Marvin for JavaScript news
Homology groups has been added
Structure Checker got an integral part of Marvin Beans
Installing Marvin Beans will install the fully functional Structure Checker application
Structure Checker:&Checker names and error messages can be localized or customized
Elemental Analysis:&Charge is taken into account in atomic mass calculation
Structure Checker:&&Copy as action string& option is available
I see that the new version of the reference management application
is now out for beta test. Reading through the release notes this looks like it will be a major upgrade, perhaps the most significant change is the use of Dropbox for syncing between devices making it easier to get access to your references. This sounds excellent however I do know of some institutions that prohibit the use of Dropbox so I was interested to see that &other cloud based syncing services in addition to Dropbox to follow&.
In addition there is:-
A fresh, new user interface: the new Papers experience is simpler and more organised.
Navigation modes to keep your work and thoughts organised.
Relevant article suggestions based on the content you are reading.
Automatic PDF download when you import articles.
Better than ever metadata discovery and matching.
Stay connected: discover tweets and posts about the articles you are reading.
View and annotate supplemental files directly within Papers 3.
Papers 3 will require Mac OS X Lion and above.
There are more reference management tool here.
we looked at using the command line tool
to calculate a number of molecular descriptors and then import them into Vortex. However there a couple of issues with doing this not the least ensuring all the environment variables are set correctly. An alternative is to use MOE as a web service and access the tools using the SOAP protocol (Simple Object Access Protocol). This
protocol provides a specification for exchanging structured information in the implementation of Web Services in computer networks. It relies on XML Information Set for its message format.
is a new web resource provided by the EBI, it is a 'Unified Chemical Identifier' system, designed to assist in the rapid cross-referencing of chemical structures, and their identifiers, between databases. Currently the uniChem contains data from 19 different databases:-
Since ChemBioDraw can generate InChi Keys I thought it might be interesting to write an applescript that access this service. The
is a short, fixed-length character signature based on a hash code of the InChI string. By definition, hashing is a one-way conversion procedure and the original structure cannot be restored from the InChiKey allowing confidential searching.
is a Mac OS X Widget that can be used to perform common actions on DNA sequences. It is useful for scientists working in genetics and can be used to obtain the complement reverse of a DNA sequence, the protein translation in all six reading frames (three in the forward strand and three in the reverse), find CpG dinucleotides and calculate the composition and the Tm (melting temperature) of a DNA molecule.
this is a mobile app for iPad, iPhone and iPod, a complement to your Labguru account, Labguru Mobile assists you with 4 essential functions: Record images of results and link them to their specific experiment, Drill down into your lab's storage locations, Manage orders and inventory with the shopping list, Retrieve protocols on your bench to execute experiments then automatically integrate results into your Labguru account
Now added to the .
3D printing is a process of making a three-dimensional solid object of virtually any shape from a digital model and I guess it is a sign that what was a bleeding edge technology has now become mainstream when the London branch of Selfridges announce that the team at , a 3D printing workshop based in Clerkenwell in London are opening an in store studio. 3D printing uses an additive process, where successive layers of material are laid down in different shapes to slowly build up the final 3 dimensional shape.
Image generously provided by Molecular Graphics Laboratory, The Scripps Research Institute
I&ve tried to pu