[Chimera-users] COX inhibitor demo discrepancy

Elaine Meng meng at cgl.ucsf.edu
Sun Sep 17 09:54:37 PDT 2017


Hi Simon,
(1) There are lots of molecular dynamics programs: AMBER, GROMACS, NAMD etc., and the list of input formats for the Chimera “MD Movie” tool shows which of those programs’ results it can handle:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

Chimera itself even has a Molecular Dynamics SImulation tool (see Tools… MD/Ensemble Analysis) but it is relatively slow. Be aware that there is a learning curve to running MD simulations.  Garbage in gives garbage out, so you have to take some time to learn about the technique and its limitations.  There are many input options and parameters, and just taking all the defaults isn’t usually the path to success for any given molecular system.  There are textbooks on the subject and running a decent simulation could be a project in itself.

Or if you just wanted a conformational ensemble rather than a trajectory, there are a whole host of other programs that do some normal mode analysis based on network models.  Those seem simpler than MD to use, but the results are more limited; that’s just a general impression… I’m not an expert on the topic.

Even simpler is if you have two different conformations of some protein, you can morph between them in Chimera and show the results in Chimera.  For example, see the “superpositions and alignments” tutorial starting at “different conformations of the same protein"
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html>

(2) References to the papers about the data are given in the MD Movie tutorial.  Part 1 uses MD results (probably from AMBER but you’d have to read the paper to doublecheck) and part 2 uses an NMR ensemble.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html>

(3) the browser is showing the text of 1plx.pdb … you just need to save it as plain text, just like you did for ras.mol2 .  Alternatively, you can get the same file from RCSB PDB, Download Files -> PDB Format:
<http://www.rcsb.org/pdb/explore/explore.do?structureId=1plx>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 16, 2017, at 2:04 PM, simon chapman <rowanlodge19 at gmail.com> wrote:
> 
> Thank you Elaine...that did it! Couldn't save as Plaintext, but it still worked as Notepad.
> 
> I am very pleased with the MD Movie tutorial...it worked for me without too many changes, and is suitably impressive. Did the authors supplying the data derive them from AMBER?  How can I supply data relevant to the molecules I'm studying to produce the appropriate MD Movie?
> 
> Also, and I hope it's OK to bother you again, the attached screenshots show the result of trying to download 1plx.pdb. I've tried several formats, but the message "no pdb structures found" appears every time.  Clicking " 1plx.pdb" in the tutorial leads to the page shown. Selecting "save as..."  leads to  the other two pop-ups in screenshot 1. Downloads lists the file as Tutorial FrameSet, and contains the four files shown in screenshot 2. Feel like I'm going round in circles with this one.
> 
> Thanks in advance...despite the challenges, Chimera is very impressive, and should enhance my MSc thesis which commences next month
> 
> Best wishes   Simon
> 



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