- Chimera-users - RBVI Mailing Lists

Showing more than a single centroid trace
by Francesco Pietra 18 Aug '11

18 Aug '11

Hello: I would like to show several centroid traces for model 0, 1, 2, .. Actually, it is the same model, differing, in the movies, for the protein fluctuations. What I did, was to superimpose movie for model 1 to the already done movie for model 0, hiding the protein for model 1 and choosing a different color for the centroid. Doing that, the instant position of the centroid can only be color-highlighted for model 0. I wonder whether there is a better procedure to show the various centroid traces above a single protein model. thanks francesco pietra

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XPLOR volumetric data not shown as a volume
by matthias.gutmann＠stfc.ac.uk 18 Aug '11

18 Aug '11

Dear all, having succeeded in writing an XPLOR data file and importing it into CHIMERA, I was expecting to see a cube like volume. Instead, I'm only seeing a thin plane. Is this to be expected? The header for the XPLOR file is as below: 1 SXD2001reciprocal_space_volume 301 0 300 301 0 300 301 0 300 30.10000 30.10000 30.10000 90.00000 90.00000 90.00000 ZYX 0 0.57280 0.05125 0.25826 0.23192 0.47232 0.40565 0.28667 0.06406 0.13678 0.22750 0.22332 0.11380 -0.02432 0.32358 0.22395 0.06303 0.22736 0.27504 0.30512 0.21062 0.26810 0.15033 0.25180 0.39434 0.85280 0.25197 0.07160 0.22430 0.28253 0.11386 0.34160 0.32177 -0.03150 0.22739 0.47072 -0.00241 0.26013 0.20844 0.20823 0.30089 0.40608 0.23863 -0.13479 0.28377 0.08277 0.25996 0.23550 0.09638 How can I get the entire volume to display as a volume rather than a single plane? Is the XPLOR format not a good one to use for this purpose? Many thanks and best wishes, Matthias ---------------------------------------------------------------------------------------------- Matthias Gutmann Instrument Scientist SXD Rutherford Appleton Laboratory Phone: +44 (0)1235 44 6397 ISIS Facility Fax: +44 (0)1235 44 5200 Chilton Didcot Office : R3, 1.28 Oxfordshire OX11 0QX Email: Matthias.Gutmann(a)stfc.ac.uk UNITED KINGDOM -- Scanned by iCritical.

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Unrecognized command: "minimize"
by Viachaslau Bernat 18 Aug '11

18 Aug '11

Dear Chimera developers, I've got a problem with scripting in chimera. By analogy with your example I've written a python script for geometry optimization of small library of ligands. In GUI mode all commands run smoothly as I type them into chimera command line. Nevertheless, when I try to run a script containing the same commands I get the error `unrecognized command: "minimize"`, no matter if I run it from GUI interface menu or with --nogui parameter. Here is my testing script (test.py): import os import chimera from chimera import runCommand as rc from chimera import replyobj os.chdir("/home/viachaslau/sybyl/sublib/") fn = "lib1.mol2" rc("open " + fn) rc("miminize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true") rc("write format pdb 0 min/" + fn + ".pdb") rc("close all") rc("stop now") And here is the output from Python: ~/sublib> ~/chimera/bin/chimera --nogui test.py Executing test.py... Opening lib1.mol2... UNQ1 opened Traceback (most recent call last): File "/home/viachaslau/chimera/share/chimeraInit.py", line 677, in init chimera.openModels.open(a, prefixableType=1) File "/home/viachaslau/chimera/share/chimera/__init__.py", line 1541, in open models = func(filename, *args, **kw) File "/home/viachaslau/chimera/share/chimera/__init__.py", line 973, in _openPython loadFunc(sandboxName, fileName, f) File "test.py", line 8, in <module> rc("miminize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true") File "/home/viachaslau/chimera/share/chimera/__init__.py", line 2235, in runCommand makeCommand(*args, **kw) File "/home/viachaslau/chimera/share/Midas/midas_text.py", line 78, in makeCommand 'Unrecognized command: "%s"' % cmd MidasError: Unrecognized command: "miminize" Error while processing test.py: MidasError: Unrecognized command: "miminize" File "/home/viachaslau/chimera/share/Midas/midas_text.py", line 78, in makeCommand 'Unrecognized command: "%s"' % cmd See reply log for Python traceback. I run SUSE 11.3 as operating system and chimera is installed into ~/chimera/ I also tried to run commands row by row in IDLE window of chimera and found out that python suspends on runCommand("minimize ...") command -- Viachaslau Bernat, PhD-student Department Chemistry and Pharmacy Schuhstrasse 19, 91052 Erlangen -- Germany Phone: +49-9131-8522588 www.medchem.uni-erlangen.de

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delete volume densities
by Hernando J Sosa 17 Aug '11

17 Aug '11

A while ago I remember using a Chimera function to delete map densities that were outside a given distance from selected atoms in a structure. I can't seem to find this utility anymore. Can somebody please remind me where to find it. Is this utility still there in the new chimera versions? Thanks Hernando

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Re: [Chimera-users] suggested feature/model panel
by Eric Pettersen 17 Aug '11

17 Aug '11

On Jan 22, 2009, at 3:15 PM, Eric Pettersen wrote: > On Jan 21, 2009, at 5:05 PM, Matthew Dougherty wrote: > > > 1) ability to create folders in the model panel so models can be > > grouped > > 2) ability to have a model in multiple folders > > 3) ability to show/hide in a folder by a a single checkbox > > 4) ability to name the folder > > These are good suggestions, and we have discussed adding some kind of > grouping mechanism in Chimera given that there are a lot of situations > where you want to treat a set of models as a single entity (e.g. > multiple structures fit into a EM map). > > I think #2 and #3 are in conflict though. Really, I don't think you > want #2 -- it's too confusing. Say a model is in two groups: you > close one group -- what happens? You hide one group -- what happens? > You deactivate one group and move the other -- what happens? Perhaps > if you elaborated on the motivation for putting a model in multiple > groups then some other alternative could be devised that provides what > you need. > > I'll open a change-request in our Trac database for "grouping > mechanism" and include the above. I don't really want to promise a > timeline, but the issue is a concern of ours. Seems like I never opened that ticket, at least I can't find it searching the database. A year later I did open a very similar ticket (#8253) which has now been implemented. So the Model Panel now supports grouping (and ungrouping) models in the current daily build, which at least minimally satisfies points 1, 3, and 4 above. The groups can be named as you wish, and changing active/shown/color/etc. for a group changes the corresponding attribute of all the models in the group. Right now if multiple models are opened from a single data source they are automatically grouped. This comes into play most often when opening NMR ensembles. If anyone has any strong opinion as to whether this is a good default behavior or not, please speak up! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Calculation of Hydrophobicity
by Magnus Andersson 17 Aug '11

17 Aug '11

Hi, I'm a new user to Chimera and found it very useful really fast. I have a question however, is possible to make a calculation of the hydrophobicity of a surface or the electrostatic potential, not only show it visually? Best regards Magnus ------------------------------------------------------------ Magnus Andersson, PhD Assistant Professor Department of Physics Umeå University SE-901 87 Umeå, Sweden Phone: +46 90 786 63 36 Mobile: +46 706 460 602 Email: magnus.andersson(a)physics.umu.se<mailto:magnus.andersson@physics.umu.se> ------------------------------------------------------------

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Problem with volumetric data in XPLOR format
by matthias.gutmann＠stfc.ac.uk 17 Aug '11

17 Aug '11

Dear all, I'm trying to write volumetric data in XPLOR format in order to import it into Chimera for displaying. The volumetric data set is a general volume data set, not necessarily an electron density map. However, it keeps on failing as Chimera keeps on thinking there are only 262 data values, whilst expecting 90601 numbers (which is the correct number). I'm trying to write the XPLOR file in the format given on the CNS web page: Format of CNS maps The grid size of the map is determined by the GRID parameter in the FFT statement. The following lines show the beginning of a typical electron density map file: 2 !NTITLE REMARKS FILENAME="" REMARKS DATE:18-Jun-98 12:24:08 created by user: 30 4 12 15 5 10 16 2 12 0.40960E+02 0.18650E+02 0.22520E+02 0.90000E+02 0.90770E+02 0.90000E+02 ZYX 0 -0.97086E+00-0.49927E+00-0.82774E+00-0.13491E+01-0.57034E+00-0.71253E-01 -0.19491E+00 0.61017E+00 0.10064E+01-0.22888E+01-0.94020E+00 0.77451E+00 0.57539E+00-0.31211E-01-0.27430E+00-0.36526E+00 0.34772E+00 0.81884E+00 -0.19954E+01-0.10117E+01 0.18038E+01 0.19008E+01 0.11886E+00-0.41646E+00 0.47560E-01 0.48855E+00 0.57606E+00-0.22320E+00-0.12787E+01 0.47590E+00 .... -9999 0.2044E-09 0.9999E+00 Is this correct or is Chimera expecting a different format? Looking forward to your replies! Many thanks and best wishes, Matthias ---------------------------------------------------------------------------------------------- Matthias Gutmann Instrument Scientist SXD Rutherford Appleton Laboratory Phone: +44 (0)1235 44 6397 ISIS Facility Fax: +44 (0)1235 44 5200 Chilton Didcot Office : R3, 1.28 Oxfordshire OX11 0QX Email: Matthias.Gutmann(a)stfc.ac.uk UNITED KINGDOM -- Scanned by iCritical.

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suggestion
by Dougherty, Matthew T 16 Aug '11

16 Aug '11

It would be good to have a session description window that I could type text into. The typical method is to generate a session file name that is the description, but as the complexity of a session file increases it would helpful to be able to write a couple sentences/paragraph as to the subtle differences it has over a near identical session file. It would also allow me to pass messages/instructions in the session file to other users so they can properly implement the session file on their computer (e.g., "be sure to change the directory name and update your density files", "the related command files that work with this session file are ....") Later on such information could be extracted in mass from closed session files, allowing for searches using database-like queries. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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BIOMT
by Ludovic Autin 16 Aug '11

16 Aug '11

Hi there, I am wondering if its possible to access the matrices computed by the sym command and/or if its possible to save the multiscale structure as a PDB with the BIOMT fields instead of the full structure? thanks in advance Ludovic

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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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centroid trace problems
by Francesco Pietra 01 Aug '11

01 Aug '11

hello: "centroid" works fine to me in getting the trace of a moving molecule in and out of a protein, using command define centroid radius 0.2 color red :residuename when the residue is unique. In fact, the method has produced extraordinarily illustrative (I am using the words of the referee) in a paper that will appear shortly on Chemistry & Biodiversity. Now I have three diatomic molecules, only one of which is made moving around. In this case define centroid radius 0.2 color red :residuename:residuenumber for the moving residue does not work. What happens is that "red balls" for the specified residue are being accumulated at the place of origin of the residue, while the residue is leaving the protein as a short bar, not a ball. Could that be fixed in the above command? thanks francesco pietra

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hide a peptide in Chimera
by C.J. 29 Jul '11

29 Jul '11

Hi,all, I have a pdb file containing several peptides. And I want to hide some of them when visualizing the file in Chimera. Anyone would like to help me to that? I'm appreciated of any suggestions. -- Regards! C.J.

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Hbond in CLI + cacheDA
by Maciek Wójcikowski 28 Jul '11

28 Jul '11

Hello everyone, I'm trying to compute hbonds for quite large molecular database, so i do it in CLI. I've added cacheDA parameter which speeds up whole process at first by 10 times, although after time cache is getting bigger and bigger operations slows down as one can expect, because Chimera is caching every compound. Is there a way to limit the size of a cache, or even better to tell chimera to cache only protein donors and acceptors? ---- Pozdrawiam, | Best regards, Maciek Wójcikowski maciek(a)wojcikowski.pl

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Chimera 1.5.3, nvidia quadro 4000 and stereo
by Veli-Pekka Kestilä 26 Jul '11

26 Jul '11

Hello, I found following problem when trying to use Chimera 1.5.3 with stereo in Nvidia Quadro 4000. When starting the chimera in windows I will get error: Error Initializing OpenGL: Couldn't configure togl widget When stating in OpenGL debug mode it starts without any problem. Nvidia driver is 275.65 and everything works in linux without problem. In Manage 3D settings I have put on Stereo Enable. Greetings, Veli-Pekka Kestilä -- University of Helsinki / Institute of Biotechnology / veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3

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gtx-470 GeForce cards
by Francesco Pietra 26 Jul '11

26 Jul '11

With GeForce2 MX200 / Debian GNU-Linux i386 wheezy I have no problems in running movie with "define centroid". In contrast, with GeForce gtx-470 (two such cards and PhenomII 1075T (six cores)/ Debian amd64 wheezy, on running movie to get the trace of the centroid, the X server hangs and the keyboard is no more sensed. I have to restart the computer from a ssh-linked desktop. In both cases chimera 1.5.3. Chimera was started as the only application, just after booting the OS (I am saying that because, to run molecular dynamics, I have first to command # nvidia-smi -L # nvidia-smi -pm 1 Any experience to this regard? thanks francesco pietra

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castp .poc file is not opened in restored session (plain text version)
by Boaz Shaanan 26 Jul '11

26 Jul '11

Hi, I save a session in which I used castp .poc file (very nice indeed!). However, after saving the session, the restored session does not open the .poc file. Is that how it's supposed to be? Cheers, Boaz P.S. sent again in plain text format since it seems the previous html version has been mangled up Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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