August 2011 - Chimera-users - RBVI Mailing Lists

Residue.uniprotIndex
by Eric Pettersen 16 Aug '11

16 Aug '11

I thought some of the script writers out there might want to know that in the latest daily builds residues have a "uniprotIndex" attribute which gives the position of the residues relative to their UniProt sequence, if the correspondence can be determined. To determine the correspondence the structure must have valid PDB HEADER and SEQRES records, and the PDB web site must be reachable (to use their UniProt mapping service). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Surface point types in WriteDMS
by Ken Shimo 11 Aug '11

11 Aug '11

Hello, When I use WriteDMS, a surface point is defined by the 7th field, which should start in 'S'. In the format definition, next to it, should be an 'S', for saddle, 'C', for contact, 'R', for reentrant, that defines de surface type. But in Chimera's WriteDMS the surface points are always set as 'C' (contact). How can I create a DMS file with the correct surface types? I'm thankful for any help, -- Helder Ken Shimo BSc in Biomedical Informatics (University of São Paulo - Brazil) MSc candidate in Bioinformatics (University of São Paulo - Brazil) -- "When I get sad, I stop being sad and be awesome instead." (Neil Patrick Harris as Barney Stinson)

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Large size display system
by jens j birktoft 10 Aug '11

10 Aug '11

Subject: Large size display system: I am looking for some advice regarding a presentation system that permit the display in high definition of interactive molecular graphic sessions (incl. Chimera) to our research group (10-12 people). Ideally we would like a 32"-36" LCD monitor coupled to a computer equipped with the proper graphics card for the large display as well as 24" monitor . Any suggestions would be greatly appreciated Cheers Jens +++++++++++++++++++++++++++++++++++++++++++++++++++++++*/ Jens J. Birktoft, Department of Chemistry, New York University e-mail: birktoft(a)nyu.edu <mailto:jens.knold@gmail.com> slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 Phone: 212-749-5057

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Problem with a script calculating distance between residues in a single pdb file with several models
by Damien Larivière 09 Aug '11

09 Aug '11

Dear all, Here is a single pdb file called modetest_14.pdb. It contains 6 structures: 1 protein MutS (only chain B) with 5 different conformations + another protein MutL (chains A and B). In Chimera, the protein with the 5 different conformations is displayed as model 0.1 to 0.5. The other protein is model 0.6. I would like to calculate the distance between the residue 239 of MutS chain B (for the 5 conformations) and the residue 169 of MutL chain A. I wrote this script which reports this error message: expected an indented block (scriptdistance.py, line 4) *from chimera import runCommand as rc rc(r"open C:\Program Files (x86)\Hex 6.3\examples\New Hex run_SL_250211\FirstRun_S_Ldimer\New_filtering\Eucl_Dist_S246-L297\Top solutions\SL0265B\dockLH248\NMA\Test\modetest_14.pdb") for i in range(1, 6): rc("distance #0.%d:239.B@N #0.6:169.A@N" % i)* May you tell me what is wrong? the script correctly opens the file so I suppose it is the python string #0.%d (intended to specify 0.1, 0.2,... 0.5)!? Thanks for your help Damien

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python and MD
by Daniel Gurnon 08 Aug '11

08 Aug '11

Hi everyone, I have a question for the python experts: Suppose I have opened an MD trajectory using MD movie. I want a script that will capture images along the trajectory spaced by user-defined timespans. Problem is, I don't know how to use a script to go to a specific frame in MD movie. As I understand it, coordset, as employed in the following example, requires the user to first play through the entire trajectory. With a million frames, that's not practical. Here's what I have so far, cobbled together from examples and my own limited understanding of Python. ---------------------------- from chimera import runCommand timestep=input ("How many picoseconds pass between frames?") spacing=input ("What spacing, in ps, do you want between structures?") start=input ("Which frame do you want to start with?") end=input ("What frame do you want to end with?") runCommand("coordset #0" + start) runCommand("focus") runCommand("copy file C:\Users\Dan\Desktop" + "\\" +start + ".png" + " width 2000 width 2000 supersample 3") ---------------------------- So in place of coordest, what could I use to jump to frames within MD movie? And while I'm at it, How can I generically specify the desktop in a windows environment (so that I could give this to a student and they wouldn't have to change "Dan" in c:\users\Dan\Desktp") How can I change the filename for the image to reflect framenumber? Thanks as always for your help. Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Python command SaveReplyLog
by Damien Larivière 08 Aug '11

08 Aug '11

Dear all, Within a loop for i in range(1, 5), I would like to save the Reply Log in text file in a specific location. My script fails when I use such syntax, saying Unrecognized command: *from chimera.tkgui import saveReplyLog rc("saveReplyLog('C:\Program Files (x86)\Hex 6.3\examples\replyLog%d.txt')" % i)* I looked at old posts saying the syntax to be saveReplyLog('path') but it does not work. May you tell me what is wrong with it? I can post the whole script if necessary. Many thanks for your help Damien

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MD setup from command line?
by Dr. techn. Thomas Mitterfellner 04 Aug '11

04 Aug '11

Hello! I'm using Chimera to view DFT optimizations and vibrational modes. I split the large xyz files into multiple small xyz files and load them with the MD tool. Now my question is: can I do the last step from the command line so I could write a script which sets the first and the last frames automatically? Also, is it possible to create the respective movie (as mpeg) in an automated fashion? Thank you, Thomas

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Fwd: [3DEM]asymmetric unit segmentation
by C.J. 03 Aug '11

03 Aug '11

Dear all, I post here for the suggestion of Steven Ludtke in the 3DEM list. best regards! C.J. ---------- Forwarded message ---------- From: C.J. <biocjh(a)gmail.com> Date: 2011/7/13 Subject: [3DEM]asymmetric unit segmentation To: 3dem(a)ncmir.ucsd.edu Dear all, Any one have a experience on segmentation of asymmetric unit from icosahedron virus structure volume? I wonder whether there is any programme could process that automatically? Any comment would be appreciated! -- Regards! C.J. -- Regards! C.J.

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Torsion adjust causes weird behavior
by Greg Friedland 03 Aug '11

03 Aug '11

Hi, I'm attempting to adjust a side chain torsion by hand for an asparagine residue but when I change it in the 'adjust torsion' panel, another residue (only one) 5 angstroms or so away is rotated around the bond axis as well. I made sure that the dihedral bond vector in the panel is pointing away from the backbone pointing in the direction and that only one torsion is selected. Is there a way I can change this behavior to only adjust the relevant residue? Thanks, Greg

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Announcement: Release of DOCK 6.5
by Scott Brozell 01 Aug '11

01 Aug '11

We are pleased to announce the release of DOCK 6.5. DOCK is a suite of programs for molecular docking. In version 6.5 a new scoring function Descriptor Score is available. It reports van der Waals and Coulombic energies, hydrogen bonds, and per-residue energy decomposition comparisons with a reference molecule. DOCK continues to provide a variety of other scoring methods including grid based, PB/SA, and GB/SA, as well as a simple interface to the AmberTools MD engine that enables receptor flexibility and a complete MM force field. For full information on what is new in DOCK 6.5, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.5.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu

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Chimera-users August 2011