If you like the "R" language, there is also Bio3D:
http://thegrantlab.org/bio3d/index.php
It has a rather nice feature that allows you to produce a movie /
trajectory of the PCA modes that can be easily viewed in VMD, which is a
neat alternative to the porcupine plots.
It can also be used to perform a lot of the other common analysis
computations such as RMSD, identification of core regions, computation of
phi / psi / chi angles, etc.
> Recently, January 4, the archived as ANN: MDTraj 0.5.0 Release.
>
> MDTraj 0.5.0 is a python library for manipulating molecular dynamics
> trajectories. The links for MDTraj 0.5.0 are:
>
> https://pypi.python.org/pypi/mdtraj (Sources and binary installers)
> http://mdtraj.s3.amazonaws.com/index.html (Documentation and examples)
>
> There is an example of PCA visualisation:
>
> http://mdtraj.s3.amazonaws.com/examples/generated/example_pca.html
>
> Regards
>
> George
> =========================================
> Hi,
>
> I'm pleased on announce the release of MDTraj 0.5.0, a python library
> for manipulating
> molecular dynamics trajectories with wide cross-format support and a
> focus on speed.
>
> Sources and binary installers can be found at
> https://pypi.python.org/pypi/mdtraj, or
> installed via easy_install / pip. Documentation, including many new
> examples, can
> be found at http://mdtraj.s3.amazonaws.com/index.html.
>
> A big thanks goes out to Kyle Beauchamp and Ravi Ramanathan for
> contributing
> patches and code reviews.
>
> -Robert
>
> What's New
> ----------------
> - Numerous bug fixes
> - Much improved coverage of the test suite.
> - Removed cffi dependency for accelerated geometry code
> - Faster multi-trajectory loading
> - MSMBuilder2 LH5 format support
> - Change license from GPL to LGPL
> - More convenience methods on Topology
> - PDB writer writes connect records
> - Hydrogen bond identification with baker_hubbard
> - Rotation/translation to superpose trajectories
> - New RMSD API. It's much simpler and much more memory efficient
> - Full support for computing all of the chi angles
> - Add seek/tell methods to all of the trajectory file objects
> - New top level memory efficient iterload method for chunked trajectory
> loading
> On 07 Jan 2014, at 15:53, Andre C. Stiel <andre.stiel.tuebingen.mpg.de>
> wrote:
>
>> Hi,
>> there are a number of questions on essential dynamics analysis and its
>> visualization in the mailing list, but I do not get really consistent
>> information from it. Most of it seems to be a little outdated. I guess
>> there are people using this technique maybe they can guide me to some
>> ideas.
>> Here is what I gathered from the archive:
>>
>> Interactive-ED (IED) ( http://mccammon.ucsd.edu/ied/) - from 2004
>> running on VMD. I didnt find newer versions or information. And it does
>> have some issues with the ptraj format as far as I understand.
>>
>> Pocubine plots: VMD plugin, pymol (using modevectors), BILD
>>
>> Are there other tools techniques? How do you visualize these movements,
>> how compatible are the afore mentioned with the cpptraj formats for
>> modes and projections?
>>
>> Maybe a little broad question but there is really not to much out there
>> on PCA - amber - visualization
>>
>> cheers
>>
>> And
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Tue Jan 07 2014 - 11:00:03 PST
