- Chimera-users - RBVI Mailing Lists

How can I calculate RMSD with chimera script
by Michał Kadlof 19 May '15

19 May '15

Hello, I have a need of calculating about 1000 of RMSDs between two particular regions of reference model and testing model. I would like to do this with chimera script. I'm using chimera-1.10.1-Headless Linux 64-bit and have no access to any GUI. Currently my script looks like this: import sys, os, re from chimera import runCommand as rc << not important stuff >> rc("open %s" % (native)) for i in models: rc("open " + i) rc("rmsd #0:{0}-{1} #1:{0}-{1}".format(s,k)) rc("close #1") rc("close all") rc("stop now") This allow me to see output on the screen, but I don't know how to capture it for further processing. I found somewhere something like this: from chimera.tkgui import saveReplyLog << do something >> saveReplyLog('replyLog.txt') But it seem to work only in versions with GUI. Please help. -- best whishes Michał Kadlof University of Warsaw

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depth cue by color for tomogram
by Michael Elbaum 18 May '15

18 May '15

Hello all, I noticed a new sort of 3D color glasses (http://chromatek.com/) that work via blue-red chromatic aberration rather than shifted pairs. I think this would be a useful addition if it isn't available already somehow. The major advantage for a lecture situation is that 2D images are visible also without glasses. I tried to encode depth by color in Chimera but was not successful. I'm using solid style with transparency to see "into" the tomogram, loaded in Volume Viewer. I'd like the deep features to be in one color and the higher parts another, with sparse regions relatively transparent. In the main Viewing panel there's an option for depth cue on the Effects tab, but the cueing is relative to the Side View orientation rather than the real depth. Also there seems to be no option for a color gradient. thanks for any help, Michael Prof Michael Elbaum Dept of Materials and Interfaces Weizmann Institute of Science Rehovot 76100, ISRAEL tel +972 (0)8-9343537 fax +972 (0)8-9344138

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Select multiscale model surface pieces with command lines
by TUBIANA Thibault CNRS 18 May '15

18 May '15

Hi everyone! I Want to script a movie, but to do so, I need to select some surface pieces of a virus multiscale model with command line. I didn't find any way to do that. I try to select them with the mouse (ctrl+click) and then rename the selection with "namesel", it works but when I save the session and reload it, theses selections are cleared.... I can't do that each times I load my session because I have plenty of them and it's to generate the movie on SSH on another computer more powerfull... I can't split them to create a new model (for exemple with coordinates) because I will have to update all my "savepos" position... Did someone know how to do that ? Thank you a lot for your help, Regards, -- Tubiana Thibault PhD Student Institut de Biologie Intégrative de la Cellule CNRS UMR 9198 CEA-Saclay, Bâtiment 532 - Pce 12A 91191 Gif-sur-Yvette 06.79.90.95.85 http://www.tubiana.me

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Problem running Chimera remotely on CentOS7 system
by "Kestilä, Veli-Pekka" 12 May '15

12 May '15

Hi, I have following error when trying to run Chimera remotely on CentOS7 system from OSX this seems to affect also Windows with Xming libGL error: dlopen /usr/lib64/dri/swrast_dri.so failed (/opt/sci/UCSF-Chimera64-1.10.1/lib/libgcc_s.so.1: version `GCC_4.7.0' not found (required by /usr/lib64/dri/swrast_dri.so)) libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: GLXBadContextTag Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1359 Current serial number in output stream: 1359 On windows the error is: ibGL error: dlopen /usr/lib64/dri/swrast_dri.so failed (/opt/sci/UCSF-Chimera64-1.10.1/lib/libgcc_s.so.1: version `GCC_4.7.0' not found (required by /usr/lib64/dri/swrast_dri.so)) libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 145 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1350 Current serial number in output stream: 1350 How I can get this to work? Intended use would be in classroom where we don't have permissions to run or install Chimera. Greetings, Veli-Pekka Kestilä -- Veli-Pekka Kestilä / Huone 4318 / Biokeskus 3 (Viikinkaari 1) / 050-3000014

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Acylation of peptide
by Remmer Salas 08 May '15

08 May '15

Hi! I am new to Chimera and I am trying to modify the PDB file of a peptide by acylation. I have also a PDB file for the fatty acid which I got by removing the bound protein. I used the join models to form a peptide bond but prompted with this error: The following problems occurred while reading PDB file for anomt1.pdbStart residue of secondary structure not found: HELIX 1 1 LEU 2 LEU 10 1 8Model 1 (anomt1.pdb) appears to be a protein without secondary structure assignments.Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3Use command 'help ksdssp' for more information.TypeError Exception in Tk callback Function: <bound method BuildStructureDialog._addParamBond of <BuildStructure.gui.BuildStructureDialog object at 0x04F9FBF0>> (type: <type 'instancemethod'>) Args: ()Traceback (innermost last): File "C:\Program Files\Chimera 1.10.1\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.10.1\share\BuildStructure\gui.py", line 313, in _addParamBond self._appbDihedral.get(), phi=self._appbPhi.get()) File "C:\Program Files\Chimera 1.10.1\share\BuildStructure\__init__.py", line 869, in cnPeptideBond cn[1].residue.phi = phi File "C:\Program Files\Chimera 1.10.1\share\chimera\phipsi.py", line 91, in setPhi _setAngle(bond, phi, getPhi(res), "phi") File "C:\Program Files\Chimera 1.10.1\share\chimera\phipsi.py", line 134, in _setAngle br.angle = (newAngle - curAngle, br.biggerSide())TypeError: unsupported operand type(s) for -: 'float' and 'NoneType' TypeError: unsupported operand type(s) for -: 'float' and 'NoneType' File "C:\Program Files\Chimera 1.10.1\share\chimera\phipsi.py", line 134, in _setAngle br.angle = (newAngle - curAngle, br.biggerSide()) My first question is how to solve this error. Second, how can I optimize the generated PDB file using Chimera? I want also to convert this optimize PDB file to PQR. Any advice is greatly appreciated.

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clip planes
by Bharat Lakhani 08 May '15

08 May '15

Dear All I want to visualize the core of my protein, Is it possible to slice the protein right into two half in order to visualize the core of the protein. I tried using chimera pre-capping model but it has not been work out well. Any suggestion on this would be great. Thanks

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Coloring selected residues based on B-factor
by Mahendra B Thapa 07 May '15

07 May '15

Dear Chimera users, While using Chimera to study a protein with 511 residues, I colored residues 1- 274 'dark grey', residues 274-417 'tan' and residues 418-511 'dark khaki'. I want to color residues, say, 313,350,412,415,485,503, from blue to red with an increasing order of B-factors, say respective B-factors are 40,13,2,21,33,6 without altering the color of other residues. I manually put these B-factors values for the corresponding residues; rest residues have no b-factor values as the structure is obtained from a simulation. I tried some unsuccessful attempts visiting some previous posts (sorry if I missed such posts close to my query). Any comments and suggestions might help me. Thank you, Mahendra Thapa University of Cincinnati,OH

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aborting a volume command
by Dougherty, Matthew T 07 May '15

07 May '15

I issued this command, which works correctly. volume #2 planes z,1,100,1,10 I try to abort it around slice 50 using freeze, which does not terminate. Is there a way to abort it? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Displaying and calculating protein surface enclosed pockets
by Matthias Fellner 07 May '15

07 May '15

Good day I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I always cite your citation for sure when I publish using your software. Normally I get very far with your tutorials but this time I failed to achieve my goal and I wanted to write a direct question. I have a protein with an active site pocket. I can display the surface of the protein and then I see the pocket inside but I am really interested in the enclosed surface = the active site pocket. How can I display the "negative" (enclosed) surface area and possibly calculate its volume. Can this be done with the pdb file or is such an analysis only possible based on the electron density. I learned how to manipulate the density map in chimera, so if this is the only way I should also be able to do it if you explain the details. If I get this done I wanted to ask if there is a way to ignore water molecules from the displaying of surfaces and later calculations or if I should simply work with a pdb which has the waters removed. Thank you Matthias Fellner

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listen selection command
by Mungo Carstairs (Staff) 07 May '15

07 May '15

Hi, I am trying out a REST listener for selections in Chimera and need help. I can talk to Chimera over REST. I can start an Http listener in Jalview - and verify it in my browser. I have sent this command to Chimera: listen start selection rest http://134.36.162.131:64745/ Then silence. I haven't managed to provoke Chimera into sending me a SelectionChanged notification. I am making selections in the Chimera window - as I can see by the 'Inspect Selection' panel. I have also started Chimera standalone (no REST service) and tried the listen command in the command line, but yet to see any output on a selection. What have I missed or how can I diagnose what I am doing wrong here? Thanks, Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> The University of Dundee is a registered Scottish Charity, No: SC015096

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