- Chimera-users - RBVI Mailing Lists

H-bond angle criteria (cut-off)
by Felipe Vasquez 02 Jun '15

02 Jun '15

Hi, I am using the H-bond function in UCSF Chimera and I noted that the relaxed parameter for angle criteria is 20 by default. However, since that I have no hydrogen atoms in the pdb structure, I assume that the angle theta (donor-hydrogen-acceptor) cannot be used by Chimera as an angle criteria, and so the psi or phi angles might be used instead. Which angle is actually used in the relaxed parameters? And most important, what is the default value of that angle (angle minus relaxing value)? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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Re: [Chimera-users] Mouse control
by Elaine Meng 02 Jun '15

02 Jun '15

Dear Prof. Szabo, I can’t see your image, but the following might help: menu: Actions… Focus - OR - command: focus … if you don’t have anything selected, either of the above should center and resize to frame all of the displayed stuff in the main window. By “selected” I mean when you Ctrl-click on something in the main window, it is highlighted with green outline. If you have something selected, you can use that same menu action to focus only on the selected part (the corresponding command would then be “focus sel”). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menuactions> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/focus.html> Then, if needed, you can enlarge by zooming with the mouse or in the Side View, or with the “scale” command. I hope this helps! For future questions, we recommend you send to chimera-users(a)cgl.ucsf.edu instead of only to me, so that others can see the answers, or give better answers than mine. Regards, Elaine —— Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 2, 2015, at 1:27 PM, A G Szabo <agszabo(a)bell.net> wrote: > Elaine > You were helpful in early April I thought I would ask another question. > > I have been working with a PDB file, 2J28, that is the structure of a > full ribosome with a Signal Recognition Protein and piece of RNA bound to > the ribosome. I figured out how to get rid of all the various parts of the > Ribosome, and visualize only the SRP and piece of RNA attached to it. > > The problem is that I can't figure out how to centre that part of the > overall structure. If I move the SRP/RNA with the wheel on the mouse it > does move to the center of the screen but in the process it becomes very > small. > > I need to be able to transpose the SRP/RNA and then enlarge it. > > Can't figure it out and while there is some stuff in the tutorials and > user info, I couldn't find anything that pertained to what I needed to > do. > > This is the SRP - RNA structure from Protein Workshop after all the > ribosomal particles were hidden. > > > > The image in Chimera is even smaller. > > Thank you again for your help. > > Arthur G. Szabo > Professor Emeritus > Chemistry > Wilfrid Laurier University > Waterloo Canada. > > <winmail.dat>

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Aligning on crystal axis
by Mohamed Noor 02 Jun '15

02 Jun '15

Hello. Is there any easy way to align the view along the crystal axes, such as the ab, ac and bc faces separately? Thanks.

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Python code problem
by Mahendra B Thapa 29 May '15

29 May '15

Dear Chimera users, The command I used was chimera --nogui test.py I tried two codes (following previous posts and tutorials in chimera) in 'test.py' as follows (i) import os from chimera import runCommand as rc from chimera import replyobj rc("open " + 'test.pdb') for i in [2011,2420]: rc("""distance #0.2:2010.B@CB #0.1:%d.B@CB""" %i) *This code gave the result as expected*: Executing test.py... Opening test.pdb... 60 models opened Distance between #0.2:2010.B@CB and #0.1:2011.B@CB: 72.346 Distance between #0.2:2010.B@CB and #0.1:2420.B@CB: 92.979 Executed test.py (ii) import os from chimera import runCommand as rc from chimera import replyobj rc("open " + 'test.pdb') for i in range(2011,2420): rc("""distance #0.2:2010.B@CB #0.1:%d.B@CB""" %i) *This code gave the result as* ' You selected %d.' % numSelected) MidasError: Exactly two atoms/axes/planes must be selected. You selected 1. Error while processing test.py: MidasError: Exactly two atoms/axes/planes must be selected. You selected 1. File "/opt/UCSF/Chimera64-1.5.3/share/Midas/__init__.py", line 1266, in distance ' You selected %d.' % numSelected) What could be the error this code? Only difference between two codes is: "for * i in [2011,2420]:" & "for i in range(2011,2420):"* That is, I am interested to use range operator in 2nd case instead of two values as in the 1st case. Thank you for help, Mahendra Thapa University of Cincinnati,OH

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Ramachandran plot for a selection
by Elena Lilkova 28 May '15

28 May '15

Dear Chimera community, First I would like to just say that I am new to Chimera. I made a MD simulation of a protein using NAMD. Now I am interested in generating a Ramachandran plot for the whole trajectory, but only for a specific selection of my protein, namely three specific residues. I fail to succeed. Could anyone probably suggest a solution? Elena Lilkova elilkova(a)phys.uni-sofia.bg PhD student, Atomic Physics Department, Faculty of Physics, University of Sofia "St. Kliment Ohridski" 5 James Bourchier Blvd. 1164 Sofia, Bulgaria Elena Lilkova elilkova(a)phys.uni-sofia.bg PhD student, Atomic Physics Department, Faculty of Physics, University of Sofia "St. Kliment Ohridski" 5 James Bourchier Blvd. 1164 Sofia, Bulgaria

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Distances in biological assembly
by Mahendra B Thapa 27 May '15

27 May '15

Dear Chimera users The biological assembly of a virus in pdb format consists of 60 models; each model with 3 chains :A, B and C. I am interested to find atoms within 4 angstroms of the atom, say CA atom of residue 2059 of chain B of model 2. The chimera crashed in graphical interface (it could be due to size of the pdb file.), so I used the following command [ http://plato.cgl.ucsf.edu/pipermail/chimera-users/2007-November/002069.html ]: chimera --nogui file_test.cmd > data_rest.log where 'file_test.cmd' consists of open test.pdb findclash #2:2059.B@CA overlap -4 hbond 0 The output file 'data_rest.log' consisted of Opening test.pdb... 60 models opened Opened test.pdb containing 60 models, 677040 atoms, and 89700 residues No contacts No contacts *I want to know whether I have used right chimera command /code. *Any suggestion might help me. Thank you, Mahendra Thapa University of Cincinnati,OH

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scale bar
by Dmitry 27 May '15

27 May '15

Dear developers, How are you? I have a question about scale bar. I am not completely sure that the scale bar I drew is correct. What are the scale settings for drawing the scale bar? By the default the scale bar is in Angstroms isn’t it? In ImageJ there is a possibility to set the scale 1 pixel = X value (nm/Å/etc) Is there the same possibility in Chimera? Thank you Sincerely, Dmitry

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Starting multiple copies of Chimera on Mac
by Tom Goddard 26 May '15

26 May '15

It is possible to run multiple copies of the same Chimera on a Mac. Here’s how. From a Terminal (/Applications/Utilities/Terminal) type the command open -n -a Chimera The -n option tells the Mac to start another copy of the application. If you prefer to start the second copy by clicking an icon then you can make that icon using /Applications/Automator, choose to make an Application, select Run Shell Script, enter the command open -n -a Chimera as the script to run, then File / Save… to save this application as “Chimera+” or whatever you want to call it. This icon always starts a new copy of Chimera so you can have as many running as you like. Tom

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Re: [Chimera-users] On the seeking of the orthologs
by James Starlight 25 May '15

25 May '15

Elaine, George, thank you very much for the suggestions and ideas!! One question- do you know some DB where is possible to seek for the orthologs (e,g based on HMM) agains *several* target sequences with flexible options like to detect minimal percent of the homology for orthologs which to be found or alternatively to make such search based on some *shared* features between those targets (e.g common structural motifs responsible for ligand binding etc) which might be specified by user initially? George, the idea to focus on particular specie seems interesting- initially I've thought in the same way but to focus on the human OR (because here I'm more comfortable with dynamical range patterns of those receptors based on the in vivo Matsunami data for instance). BTW briefly have a look on those DB I didn't find there engine to seek for the orthologs agains given target. Doest this option really exist within it? All the best, James 2015-05-22 21:10 GMT+02:00 George Tzotzos <gtzotzos(a)me.com>: > I would start from BioMart. I’m also working on OR (albeit insect ones). Try also MGI (Mouse Genome Informatics). Starting from mouse Ors you can scoop orthologs in other mammalian species. > > Cheers > > George > >> On 22 May 2015, at 18:44, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi James, >> Your questions are more about bioinformatics project design rather than Chimera use. >> >> Chimera provides basic BLAST searching of NCBI’s “nr” and “pdb” sequence databases, but these are the same databases generally used by BLAST whether you use it from Chimera or from another program, or stand-alone. Also, Chimera can fetch specific individual sequences from UniProt based on UniProt identifier, but that isn’t searching, it is just getting data you already knew you wanted. >> >> I believe NCBI’s “nr” and UniProtKB are both meant to be comprehensive (cover “all” sequences) but in their own ways, and you would have to go to those resources or their publications to learn the details. There are probably also specialized GPCR and/or olfactory receptor sequence databases. Then there are multiple ways of searching, with individual sequences or with derived patterns such as hidden Markov Models (HMMs). This is a really broad topic and in my opinion, beyond the scope of this forum. You’ve probably done some of this already, but I would recommend reading similar studies in quality journals by authors you respect, to see how they have designed their projects. >> >> Chimera doesn’t have HMM-related tools or evolutionary trace, it just allows conservation analysis on your whole alignment, or subsets of that alignment opened in separate windows. >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On May 22, 2015, at 9:22 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: >> >>> Dear Chimera users! >>> >>> I'd like to ask some suggestion regarding my bioinformatician task and >>> possible ways of its realisation using some bioinformatics methods >>> implemented in Chimera. >>> >>> 1)I need to seek for some sequence database (here I don't know >>> absolutely how to do it) of the olfactory receptors and to select 10 >>> sequences of the Ors corresponded to 10 different mammalian species -> >>> according to my idea it should be very different species associated >>> with different ecological niches so its olfactory spectrum should vary >>> dramatically. >>> Here the question: in what DB such search should be better with the >>> inclusion of flexible search criteria's like what I've listened above? >>> >>> 2)After allocating of those 10 sequences I should to find *all* >>> possible orthologs against them-> to find all OR in another species >>> which have conservation degree agains target above chosen threshold . >>> Eventually I'll need to make some analysis regarding overall >>> conservation of the OR within different species and to point out what >>> OR are most important (conservative) in different organisms in >>> accordance to some pre-defined criteria's (i.e ecological niche of the >>> species because it's associated with the odor spectrum). Here the >>> question: would the methods like blast-search be enough for such task >>> or I should to use also methods like evolutional tracing (to find all >>> important residues in different OR which tend to co-evaluate) based on >>> its alignment data? >>> >>> I would be very thankful for any suggestion! >>> >>> James >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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On the seeking of the orthologs
by James Starlight 22 May '15

22 May '15

Dear Chimera users! I'd like to ask some suggestion regarding my bioinformatician task and possible ways of its realisation using some bioinformatics methods implemented in Chimera. 1)I need to seek for some sequence database (here I don't know absolutely how to do it) of the olfactory receptors and to select 10 sequences of the Ors corresponded to 10 different mammalian species -> according to my idea it should be very different species associated with different ecological niches so its olfactory spectrum should vary dramatically. Here the question: in what DB such search should be better with the inclusion of flexible search criteria's like what I've listened above? 2)After allocating of those 10 sequences I should to find *all* possible orthologs against them-> to find all OR in another species which have conservation degree agains target above chosen threshold . Eventually I'll need to make some analysis regarding overall conservation of the OR within different species and to point out what OR are most important (conservative) in different organisms in accordance to some pre-defined criteria's (i.e ecological niche of the species because it's associated with the odor spectrum). Here the question: would the methods like blast-search be enough for such task or I should to use also methods like evolutional tracing (to find all important residues in different OR which tend to co-evaluate) based on its alignment data? I would be very thankful for any suggestion! James

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clustering
by Rafael Rocha 22 May '15

22 May '15

hello, I have a set of ligands that share Some atoms in common. How I can clustering only those atoms? Also, how I can change the variation of RMSD for this cluster analysis in the "ensemble cluster" tool of chimera? Thanks, Rafael.

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chimera improvment suggestion
by Michał Kadlof 21 May '15

21 May '15

I have small improvement suggestion: Is it possible to display directories in Open File dialog with different font than files, for example bold? I'm loosing a lot of time on scrolling my directories tree to find particular file to open. Highlighting of directories would be very handy. -- best Michał

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Re: [Chimera-users] How can I calculate RMSD with chimera script
by Eric Pettersen 19 May '15

19 May '15

Since runCommand() doesn't return any value, you need to call the underlying Python rmsd() function, which isn't hard to do. Somewhere at the top of your script put: from Midas import rmsd and then replace: rc("rmsd #0:{0}-{1} #1:{0}-{1}".format(s,k)) with: val = rmsd("#0:{0}-{1}".format(s,k), "#1:{0}-{1}".format(s,k)) --Eric On May 19, 2015, at 12:45 PM, Michał Kadlof <ramidas(a)gmail.com> wrote: > Yes it work, but then I have to write and run another script to parse output from chimera which cost HDD access time. I was wonder, if it possible to do it in single script without dumping output to separate file. > > -- > Michał > > 2015-05-19 18:53 GMT+02:00 Eric Pettersen <pett(a)cgl.ucsf.edu>: > Hi Michał, > Redirecting output from a program into a file is pretty easy in any Unix/Linux shell. This would redirect Chimera's non-error output into a file named "chimera-output.txt": > > chimera chimera-arguments-you-normally-use > chimera-output.txt > > You can also redirect the error output, but the syntax for that depends on the shell you are using. You should be able to easily Google it if you need to do that. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On May 19, 2015, at 1:16 AM, Michał Kadlof <ramidas(a)gmail.com> wrote: > >> 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 >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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Load AMBER parm/traj from command line.
by ros 19 May '15

19 May '15

Hello! Is it possible to start up chimera and have it load an AMBER topology and trajectory file? For example, in Linux, you can start VMD with: vmd -parm7 name.prmtop -netcdf traj.nc And will load the topology with the corresponding trajectory frames. In chimera we do that using the 'Get Ensemble info' window in the MD movie tools. Is it possible to do it in a single line? Thank you! Rodrigo.

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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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Re: [Chimera-users] [chimera-dev] VolumeEraser
by Tom Goddard 06 May '15

06 May '15

Hi Alex, Surfnet in Chimera does not produce a volume, only surfaces. It calculates the volume but then computes surfaces and deletes the volume. If you would to measure the enclosed volume of the disconnected pieces produced by surfnet, first make those pieces independently selectable with command sop split #0 where #0 is the id for the surfnet model (use Favorites / Model Panel to find the correct id number). Then select the piece of interest (ctrl click on it), then get its enclosed volume with command measure volume sel To type commands to Chimera use menu Favorites / Command Line. This question belongs on the chimera-users mailing list, not the chimera-dev list which is for programming issues. Tom > On May 6, 2015, at 8:18 AM, Alex wrote: > > Dear Sirs, > I recently started using chimera, please apologise my lack of knowledge. > In order to erase a surfnet volume I am trying to use the Erase volume module, but it doesn't work. Are the surfnet objects available to be used in VolumeEraser functions? Is there another way to study volume intersections? > If you know, please point out the article which describes the procedure for this kind of volume calculation. > > Best regards, > Alex > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev>

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PC shut down automatically while using Chimera
by kzhang＠mrc-lmb.cam.ac.uk 06 May '15

06 May '15

Dear Chimera Developers, Recently, I found something really annoying when I was using Chimera. The problem is that when I use chimera to display CryoEM maps(400X400X400, 32 bits), my computer shut down automatically. I don't think there's something wrong with the hardware and coot or pymol is fine. This is not just an accident. It happened quite a few times, especially when I suddenly zoom in, computer is suddenly shut down. Later there would be some error massage related to the instability of the power, CPU self protection "£$%^&# ... when I turned on the computer again. But I don't think there is anything wrong with the power as well, I've run other softwares without any problem. Also, it happens to both Window 7 and CentOS 6.5 in the same PC. So it's obviously hardware level issue related to Chimera. My guess is that there might be something in Chimera that activated the self-protection of CPU or similar things. Any ideas why this occurs and how can I solve it? Best wishes Kai

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imod
by Dougherty, Matthew T 04 May '15

04 May '15

I have recently been getting some imod segmentation files and have been noticing three problems 1) when I read the MRC and imod files I am having a scaling problem, and the datasets do not integrate. For example, if the MRC voxel size is 31.22 31.22 31.22, and the origin index is 0 -114 0, I have to change the the voxel size to 3.122 3.122 3.122 , and the origin index to 0 0 0 so that graphics match correctly. Since there are number of people in the data chain before it gets to me, I thought it might check to determine if this is known problem before going upstream to unknown people to figure out if they are getting the imod output settings correct. 2) The graphics performance with imod segmentation files is sluggish in chimera, not sure what it is in imod. I assume that the format defines the vertices at the highest resolution corresponding with the MRC file. Is there a way to improve the performance on the chimera side? I am not using contouring, just reading the file in default mode. 3) The segmentation has a lot of components, such as vesicles and microtubules, that have different colors. Is there a way to break apart the components so they can be manipulated seperately? E.g., display/hide, change colors, translate and rotate. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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running script + recording movie
by Dmitry 04 May '15

04 May '15

Dear colleagues, Does anybody know how to run the script in chimera - *.cmd (from windows) and in the same time record everything that script does as a movie? Sincerely, Dmitry

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chimera meeting tomorrow
by Greg Couch 29 Apr '15

29 Apr '15

The agenda is available in advance! Thank you Conrad! Conrad says "feel free to add items" :-) https://plato.cgl.ucsf.edu/trac/chimera2/wiki/2015-4-30

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Auto dock Vina Increasing Exhaustiveness
by Tunc Morova 29 Apr '15

29 Apr '15

Hello! I am using UCSF Chimera, Autodock Vina extension for obtaining conformations of my protein and ligand. In this interface, As you know, I can change the exhaustiveness value between 1-8. However, since my system is more than 30x30x30 A, I need to get my exhaustiveness value more than 8 for getting more accurate results. But I can’t make it more than 8 through Auto dock Vina interface in Chimera. How can I increase this exhaustiveness value ? Btw, Instead of using Opal web service, I am using vina locally. Thank you many times for your help Best Regards Tunc Morova

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Converting sdf file into mol2 format
by Mahendra B Thapa 29 Apr '15

29 Apr '15

Dear Chimera users, I am trying to convert sdf file ( downloaded from* diversity set* data from 'http://scs.illinois.edu/htsf/compound_collection/nci.php') into mol2 format. When I ran the command chimera --nogui processSDF.py as given the previous posting ( http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-March/004974.html) I got the following error messages: Cannot find consistent set of bond orders for ring system containing atom #0.73:1@N1 --- Unknown redo atom type: N3 Traceback (most recent call last): Any suggestions for correcting these errors will be a good help for me. Thank you, Mahendra Thapa University of Cincinnati,OH

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Create an artificial bond between ribbons for 3D printing
by David Bhella 28 Apr '15

28 Apr '15

Dear Chimera users, I am trying to prepare a ribbon diagram for 3D printing. As the molecule is a trimer, I would like to create a join between the ribbons such that the model is sent to the printer as a single part. So, I thought that I might be able to create a bond, but I suspect that the current tools may not be able to achieve this. Ideally I don’t want to have to show side chains, moreover the bond needs to be preserved when exported as STL format and finally it will be quite long. The only tool that would seem to come close to my requirement is the distance measure, however I can’t see how to convert that pseudo bond to a cylinder that will be exported. Any suggestions would be gratefully received. Thanks, D. Dr David Bhella MRC-University of Glasgow Centre for Virus Research Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch

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Delete Bug?
by Korbin West 27 Apr '15

27 Apr '15

Hi all, I'm running some code on Chimera to select only certain chains and nearby aspects, but when I try to delete the extraneous information, Chimera freezes up. I'll detail the commands I use below, and for reference I'm interested in the H chain of 1CT1, but it doesn't seem to work with any of its chains. open 1CT1 zonesel :.h 3.5 extend true select invert del sel It then freezes on del sel. I've tried this with other pdb files and it works fine, but for some reason it stops on this one. For example, it works fine on 1PZ3 for its A and B chains. Is this some kind of bug or is there a work-around to this issue? We looked at the residues and couldn't find anything out of place, so we are not sure what is happening. Much thanks in advance. Best, Korbin West? Wabash College

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Making a composite residue
by Repic Matej 23 Apr '15

23 Apr '15

Hello, I wonder if it is possible to construct a composite residue from two existing residues in Chimera? What I would like to do is concatenate residues ALA100 (mid chain) and GLY200 (end of chain) to make a composite residue AGL100. Chimera won't let me set the same residue number via the "resrenumber" command. Preferably, the composite residue would have all the atoms listed where ALA100 was in the original pdb. While I realize there are trivial text editor-based workarounds I would like to know if there is a native way. Thank you all, ---------------------------------------- Matej Repic Ecole Polytechnique Fédérale de Lausanne SB - ISIC - LCBC BCH 4108 CH - 1015 Lausanne ----------------------------------------

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about volume viewer
by 张雷 21 Apr '15

21 Apr '15

Hi, the experts of Chimera, I am a new user of Chimera and have a question to consult you. When I display a 3D model in the volume viewer, I found that there was an original value of the level, as the attached figure shown. If I increased and decreased the values of level, the densities of 3D models were different. Therefore, how to deternime the right value of level for a protein. It is known that the average density of proteins is 1.35 g/cm3; If a protein has a molecular weight of 1350 kDa, and 1 Da = 1.66054E-27 kg; therefore, the protein volume is 1661 nm3.If I want to display the volume of 1661 nm3 in chimera, how can I decide the value of level? In another words, how can I calculate the value of level from the actual volume of a protein? Thank you! Best wishes! Lei Zhang Peking University, Beijing, China

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Re: [Chimera-users] coloring individual segments of a protein
by Greg Couch 21 Apr '15

21 Apr '15

To get a different resolution than 72 dpi, you need to turn on the "Use print units" option in the Save Image dialog, and set the "Print resolution" and pick the image width and height. Or you can use a program like Adobe PhotoShop or GIMP to edit the DPI if you already have an image that you like. HTH, Greg On 04/21/2015 03:01 PM, A G Szabo wrote: > Greg > > Thanks for your reply > > > I had just sent Elaine another question that perhaps you might be able to > answer. > > I am currently writing a book and the editor would like the protein > structure images saved with at 300 dpi. When I saved an image of > Ribonuclease, PDB 5RSA, both as a png file and a Jpeg file the editor > indicated that the resolution was not sufficient and was only 72 dpi. > > Suggestions? > > Thanks > > ags

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Residue Numbers vs. Residue Codes
by Korbin West 21 Apr '15

21 Apr '15

Hi all, I'm trying to determine uncommon ligands in pdb files using a python code, but have run into an odd dilemma. In my code, I open a pdb in Chimera, select the ligand, and write out the residue list. However, the formatting of this list changes depending on how I run the program. If I run the program through xterm, it will print out only residue numbers. If I run the program though Chimera's Idle, however, I will get the residue codes and the residue numbers. For example, I ran this with 3VKG, you can see the results in the attached files, where I show a sample code of what I'm using, the xterm results and the Chimera results. I want to do this for a large number of pdbs, so I'd like to do this --nogui through xterm, but I need the residue codes. Has anyone else ran into this problem or know of a work-around? Thanks in advance. Best, Korbin West Wabash College

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coloring individual segments of a protein
by A G Szabo 21 Apr '15

21 Apr '15

How do I use Chimera to color a protein in the following way: for example: Helix 1 - red Helix 2 - yellow Helix 3 - magenta Strand 1 - dark blue Strand 2 - cyan Etc. A G Szabo

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keyboard accelerators
by Dougherty, Matthew T 20 Apr '15

20 Apr '15

Hi, had a few questions about the documentation. A click in the graphics window may be required. Sometimes it is necessary to click in the graphics window to take back focus from some other dialog so that accelerator or command keystrokes will register. >> is there a way to send accelerators through the Viewing-Side View? I have been dedicating one monitor for the 3D graphics and the other for control, menus, etc. using various USB devices sending accelerators. Would prefer not put to the focus/mouse cursor on the 3D graphics. Accelerators could be shown on menu entries. The keyboard shortcuts could be shown on the corresponding menu entries to make them easier to learn.? >> How? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Help in MD movie
by Ankit Agrawal 18 Apr '15

18 Apr '15

Hi I have trajectory file from gromacs and opened in chimera. Now I am doing inertia calculation. I wrote a python script to show the ellipsoid. But this script is showing only the ellipsoid. I want ellipsoid as well as the molecular structure of that frame, i.e. both ellipsoid and the molecule. so that I can show the how molecule is changing its position. This is like a structure overlay but I want it with ellipsoid. thanks regards Ankit Agrawal

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Reducing the map to a cubic box
by Sushree Tripathy 17 Apr '15

17 Apr '15

Hi, I went through the chimera user's guide and as per the syntax used "vop boxes #0 #0 useMarkerSize true" or "vop boxes #0 #0 size 36" (the simplest case) to create a cubic box from my density map (54, 36, 51). It is neither giving me any error nor giving me the output map. Please help. Thanks Sushree. Sushree Tripathy Graduate Student Department of Physics University at Buffalo

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Generating a map from atomic molecule
by Tom Goddard 17 Apr '15

17 Apr '15

Hi Zhihai, The reason your map surface shows the triangulation is because the grid spacing is large. You made the map with molmap with 30A resolution. By default molmap sets the grid spacing to 1/3 of the requested resolution, so 10 Angstroms in this case. Apparently this is too coarse for your needs. So spedify a finer grid spacing in the molmap command. For instance molmap #0 30 gridSpacing 3 to produce 30 A resolution with 3 A grid spacing. Here is the molmap documentation http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/molmap.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/molmap.html> Tom > On Apr 16, 2015, at 8:45 PM, 李智海 wrote: > > Hi Tom, > It seems that the low-resolution (about 30A) map generated from atomic model by “molmap" has many artifacts on its surface (see first attached figure), and I can see many rectangle signatures of it in Fourier space (see 2nd attached figure) so that I can not use it as the start map for further reconstruction. > Please tell me how can I get rid of this. Thank you! > > Best wishes! > > > Zhihai Li > > <molmap_30A.png><FFT.png> > > Zhihai Li > > Ph.D student in State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics. > School of Life Sciences, Xiamen University. > Xiang'an Road(South), Xiang'an District, Xiamen City, > Fujian Province, China. > >> On Apr 15, 2015, at 1:28 AM, Tom Goddard wrote: >> >> Hi Zhihai, >> >> If you want the map computed from an atomic model but on a grid that matches a reference map then you should compute the map with molmap and then resample it on the reference map grid. If #0 is the atomic model and #1 the reference map. >> >> molmap #0 8 edgePadding 50 >> vop resample #0 onGrid #1 >> >> Here the 8 is the resolution for the computed map and 50 Angstroms controls how far beyond the molecule bounding to compute the map. >> >> Tom >> >> >> >>> On Apr 13, 2015, at 9:00 PM, 李智海 wrote: >>> >>> hi, >>> here I want to generate a density map from a atomic model in Chimera, then convert the generating map into .pif file to do as the initial map performing in Auto3dem. >>> I have met some questions to successfully finish these work. >>> >>> 1.How can I generate a mol-map from a fitting model with identical dimensions, center coordinates and pixel size of its reference map. I have tried to use “Fit in map”, but the generating map differed from its fitted map in the map size. >>> >>> 2. The mrc map created in Chimera has dimension of even number of columns. If I set the column number to odd number, is it ok (for example, if the origin is off by half pixel?). The reason I am asking such a question is that I will convert this mol-map to pif format, and pif format map has dimension of odd number columns. >>> >>> >>> Thanks in advanced! >>> >>> Best wishes! >>> >>> Zhihai Li >>> >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >> >

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on script which can be read and executed by chimera
by Smith Liu 17 Apr '15

17 Apr '15

Dear All, Will you please introduce to me a web link on how to compile and edit scripts which can be read and executed by Chimera? I am looking forward to getting your reply. Smith

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the "select" funtion of mouse is disable
by sunyeping 16 Apr '15

16 Apr '15

Dear all,I find the "select" funtion of mouse in Chimera is disable. I can not use "ctrl+left mouse button" to select any item in the structure. Have you met this problem before? My systems is windows 7 and the Chimera version is 1.10.1. How to solve this problem? Do I need to change some setting?Best regards,Yeping Sun Institute of Microbiology, Chinese Academy of Sciences

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Re: [Chimera-users] Reducing the map to a cubic box
by Tom Goddard 15 Apr '15

15 Apr '15

In Chimera “atoms” means an atomic model, for example from a PDB file, not a density map. If you want to reduce your map to a cube by cropping and it is size 54,36,51 use command volume #0 region 0,0,0,35,35,35 That gets the lower left corner. To get the center part volume #0 region 9,0,7,44,35,42 The 6 numbers are imin,jmin,kmin,imax,jmax,kmax where i,j,k are indices along the 3 map axes. You can also do this with the Volume Viewer dialog menu entry Features / Region Bounds, or interactively with the mouse using Features / Subregion Selection. For more info about map manipulations http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html Tom > On Apr 15, 2015, at 1:17 PM, Sushree Tripathy wrote: > > Hi, > > Thanks for your prompt reply. What I am trying to do is I have a map which I have loaded in chimera as #0. Now I want to reduce it to cubic size. Since the syntax is "vop boxes <> volume-spec atom-spec <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> size d", so I am choosing #0 for my volume and all the atoms in that volume. so #0 again. Please correct me if I am wrong. > > > Thanks > Sushree. > > Sushree Tripathy > Graduate Student > Department of Physics > University at Buffalo > > On Wed, Apr 15, 2015 at 4:13 PM, Tom Goddard wrote: > Hi Sushree, > > Why does your "vop boxes” command use model #0 for both the map and the markers? That can’t be right. If your marker(s) are in model #1 you would need “vop boxes #0 #1 size 36”. What are you trying to do? > > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#boxes <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#boxes> > > Tom > > > >> On Apr 15, 2015, at 1:03 PM, Sushree Tripathy wrote: >> >> Hi, >> >> I went through the chimera user's guide and as per the syntax used "vop boxes #0 #0 useMarkerSize true" or "vop boxes #0 #0 size 36" (the simplest case) to create a cubic box from my density map (54, 36, 51). It is neither giving me any error nor giving me the output map. >> >> Please help. >> Thanks >> Sushree. >> >> >> Sushree Tripathy >> Graduate Student >> Department of Physics >> University at Buffalo >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > >

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Reducing the map to a cubic box
by Sushree Tripathy 15 Apr '15

15 Apr '15

Hi, I went through the chimera user's guide and as per the syntax used "vop boxes #0 #0 useMarkerSize true" or "vop boxes #0 #0 size 36" (the simplest case) to create a cubic box from my density map (54, 36, 51). It is neither giving me any error nor giving me the output map. Please help. Thanks Sushree. Sushree Tripathy Graduate Student Department of Physics University at Buffalo

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generating a map from a atomic model with the same size of its reference map
by 李智海 14 Apr '15

14 Apr '15

hi, here I want to generate a density map from a atomic model in Chimera, then convert the generating map into .pif file to do as the initial map performing in Auto3dem. I have met some questions to successfully finish these work. 1.How can I generate a mol-map from a fitting model with identical dimensions, center coordinates and pixel size of its reference map. I have tried to use “Fit in map”, but the generating map differed from its fitted map in the map size. 2. The mrc map created in Chimera has dimension of even number of columns. If I set the column number to odd number, is it ok (for example, if the origin is off by half pixel?). The reason I am asking such a question is that I will convert this mol-map to pif format, and pif format map has dimension of odd number columns. Thanks in advanced! Best wishes! Zhihai Li

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generating a map from a atomic model with the same size of its reference map
by 李智海 14 Apr '15

14 Apr '15

hi, here I want to generate a density map from a atomic model in Chimera, then convert the generating map into .pif file to do as the initial map performing in Auto3dem. I have met some questions to successfully finish these work. 1.How can I generate a mol-map from a fitting model with identical dimensions, center coordinates and pixel size of its reference map. I have tried to use “Fit in map”, but the generating map differed from its fitted map in the map size. 2. The mrc map created in Chimera has dimension of even number of columns. If I set the column number to odd number, is it ok (for example, if the origin is off by half pixel?). The reason I am asking such a question is that I will convert this mol-map to pif format, and pif format map has dimension of odd number columns. Thanks in advanced! Best wishes! Zhihai Li

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Fitting pdb model into difference map
by Chinaza Egbuta 13 Apr '15

13 Apr '15

I generated an Fo-Fc difference map using CCP4i and was able to superimpose the PDB model structure onto the map in Coot but I am unable to do so with Chimera. The model and map are offset/rotated away from each other and I have not been able to fit the model into the map with Volume Viewer --> Tools --> Fit in Map. Please let me know how I can get around this issue. Thank you. CE

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Extracting masked map region using selected sop piece?
by Oliver Clarke 13 Apr '15

13 Apr '15

Hi all, I find the sop command (particularly 'sop split' and 'sop hideDust metric volume rank') to be very useful for viewing a molecular envelope at a low threshold in an otherwise noisy map. I would like to save the volume enclosed by a single sop piece as a separate volume, but it does not seem like this is possible - when I select a sop piece and use 'volume nameregion’ to assign it a name, and then attempt to write just that region to an mrc, it saves the whole map. Is there some way to do this that I am missing? I realize that a similar outcome can be achieved with segger, but for larger maps this can be very slow (and potentially involve multiple cycles of selection and regrouping), whereas sop operations are almost instantaneous, so I feel it would be a valuable adjunct capability to that offered by segger. Also, the behaviour of sop split seems a little counterintuitive to me. When I use 'sop split' on a volume, it generates a new model with a different ID for the split map - fine so far. However, the original map seems to be completely invisible - it is listed as displayed in the model panel, but if I undisplay the split map in the model panel and toggle display of the original map in the model panel, nothing happens. If I go to the volume viewer, the original map is listed as displayed, and if I toggle it off and then on again there, it reappears. It seems like it would be maybe simpler for the user to just automatically undisplay the original map upon creation of the sop split map, but not to prevent the user from redisplaying it in the model panel. Here is a link to a screen recording demonstrating what I mean: https://www.dropbox.com/s/g40u9dhj0xslcbf/sop_split.mov?dl=0 <https://www.dropbox.com/s/g40u9dhj0xslcbf/sop_split.mov?dl=0> Best, Oliver.

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