- Chimera-users - RBVI Mailing Lists

Set interatomic distances
by George Patargias 19 Nov '13

19 Nov '13

Hello Do you know if there is a way to set interatomic distances to a certain value in chimera (rather than measuring them)? Basically what I want to do is rotate/translate a peptide with respect to a protein so that a set of interatomic distances between the two are satisfied Many thanks! George Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568

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measuring distances
by Ryan Pavlovicz 19 Nov '13

19 Nov '13

Hi, I am trying to measure the distance between two atoms from many different PDB structures using a python script. Using a command like: chimera.runCommand('distance #0:1@C1 #0:1@C2') will correctly output the distance within a tenth of an angstrom, however, i would like to output a more accurate measurement (more decimal places). Is there a way to do this when using chimera within a python script? Thanks for your help, ryan

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Commands for label formatting (font size etc)
by Andreas Göransson 18 Nov '13

18 Nov '13

Hi! How do I set font size for label / rlabel command in a command file? Can't find info in the documentation or in the mail list archive. Thanks, Andreas

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WebGL
by Hansen, Bryan (NIH/NIAID) [F] 18 Nov '13

18 Nov '13

Hi, I'm trying to export a scene using the WebGL feature within Chimera, but something seems to be going wrong. I'm attaching what opens up after Chimera saves the scene. I'm not able to rotate the output at all either. Is there a setting I need to change somewhere within Chimera? Thanks for your help and input. ************************** Bryan Hansen Microbiologist Electron Microscopy Lab NIH/NIAID/Rocky Mountain Laboratory 903 S 4th St Hamilton, MT 59840 (406) 363-9202 *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************

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Changing default max number of histograms shown
by Joel Meyerson 18 Nov '13

18 Nov '13

Hi, By default, Chimera displays up to 3 histograms in the "Volume Viewer". I know that this number can be increased manually in the "Data display options" after launching the program, but I would like to change the default number. Is there a built-in Chimera preference to set the default number to something higher? If not, can you perhaps suggest how this might be scripted to happen upon launching the program? Thanks, Joel

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Multi-fragment fit in map
by Paolo Swuec 18 Nov '13

18 Nov '13

Good morning, I am EM user and I was wondering wether is possible in Chimera to fit multiple pdb in the same volume (e.g. Fitting two monomers into a dimer map without overlaps and clashes). I am using Situs and the collage command, but I was wondering if there was an easy way of doing it in Chimera. Thank you very much, Paolo Paolo Swuec, Ph.D. Student Architecture and Dynamics of Macromolecular Machines London Research Institute Clare Hall Laboratories Cancer Research UK South Mimms Herts EN6 3LD, UK E-mail: paolo.swuec(a)cancer.org.uk<mailto:alessandro.costa@cancer.org.uk> NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103) A company limited by guarantee. Registered company in England and Wales (4325234) and the Isle of Man (5713F). Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.

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Question on labeling residues on a single-chain protein
by J. David Puett 15 Nov '13

15 Nov '13

I wish to label certain residues and have these appear along with the structure. I have used the Command line to enter the following. rlabel Met_71.A What other Command(s) is required to display and later print the labeled structure? Many thanks!

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Measure buried area
by Jian Guan 15 Nov '13

15 Nov '13

Hi all, I use measure command to calculate the buried area between capsomer and Fab. My input file is pentamer.pdb and Fab.pdb. I made surface model for them respectively and use the command line as shown below: measure buriedArea #3 #2 probeRadius 1.4 However, it replied as "Surface calculation failed" I tried also delete all non-binding units in the pentamer, it still can not work. Does anyone know how to deal with that? Thank you so much. Sincerely yours, Jian

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Re: [Chimera-users] Residue selection
by Mark Girvin 14 Nov '13

14 Nov '13

Thanks for the info Eric, - Mark ________________________________ From: Eric Pettersen [pett(a)cgl.ucsf.edu] Sent: Thursday, November 14, 2013 3:43 PM To: Mark Girvin Cc: George Tzotzos ‎[gtzotzos@me.com]‎ Subject: Re: [Chimera-users] Residue selection Yeah, waters with a blank chain ID are put in chain "water" and similarly residues in HETATM records with a blank chain ID are put in chain "het". If the chain ID is non-blank, both get assigned the given chain ID rather than "water" or "het". --Eric On Nov 14, 2013, at 12:22 PM, Mark Girvin <mark.girvin(a)einstein.yu.edu<mailto:mark.girvin@einstein.yu.edu>> wrote: Got it. And no problem - just not quite expected. So then chimera sets up internal chain names (like "water") for some entries in PDB files? I don't think George's file had any internal chain entries, or HETATM lines. - Mark ________________________________ From: Eric Pettersen [pett(a)cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>] Sent: Thursday, November 14, 2013 2:50 PM To: Mark Girvin Cc: George Tzotzos; chimera List Subject: Re: [Chimera-users] Residue selection Yeah, the :127@O behavior is deliberate. If you omit the chain ID, it only matches single-character chain IDs (i.e. not chain ID "water" or "het"). This choice was made so that if your structure has a bunch of waters that so happen to have the same numbers as various polymeric residues, :127 will get the polymeric residue(s) but not the waters. This behavior was more important before the PDB remediation a few years back where such occurrences were commonplace. Now, in standard PDB files waters are frequently assigned specific chain IDs and therefore have different numbers than the polymeric residues. Chimera's behavior still matters for non-standard PDB files generated by various programs. If I were making the decision about Chimera's behavior today, given that the issue no longer affects standard PDB files, it might go the other way (it might not), but I don't feel strongly enough to change anything. A bunch of complaining could change my mind. :-) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu<http://www.cgl.ucsf.edu/> On Nov 14, 2013, at 7:44 AM, Mark Girvin <mark.girvin(a)einstein.yu.edu<mailto:mark.girvin@einstein.yu.edu>> wrote: I don't know why that doesn't work, but: select :WAT@O seems to (if you only have the one water in your pdb file), as does: select :127.water@O (which would presumably limit the selection to the one water molecule) - Mark ________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu<mailto:chimera-users-bounces@cgl.ucsf.edu> [chimera-users-bounces(a)cgl.ucsf.edu<mailto:chimera-users-bounces@cgl.ucsf.edu>] on behalf of George Tzotzos [gtzotzos(a)me.com<mailto:gtzotzos@me.com>] Sent: Thursday, November 14, 2013 8:08 AM To: chimera List Subject: [Chimera-users] Residue selection I'm attaching a pdb file of a protein ligand complex with a single conserve water molecule. The pdb file was constructed with Antechamber Leap. The water molecule is numbered as residue 127. When I try to select using: select :127 nothing happens. Selection works with: select :WAT The problem is that I need to monitor the distance between :127@O and a particular atom in the binding site of the protein during an MD trajectory. My question is if I'm doing something wrong with the residue selection. Many thanks in advance for your help Regards George _______________________________________________ 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 _______________________________________________ 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

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Residue selection
by George Tzotzos 14 Nov '13

14 Nov '13

I'm attaching a pdb file of a protein ligand complex with a single conserve water molecule. The pdb file was constructed with Antechamber Leap. The water molecule is numbered as residue 127. When I try to select using: select :127 nothing happens. Selection works with: select :WAT The problem is that I need to monitor the distance between :127@O and a particular atom in the binding site of the protein during an MD trajectory. My question is if I'm doing something wrong with the residue selection. Many thanks in advance for your help Regards George

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Re: [Chimera-users] Issues with characters on command line (OS X 10.9)
by Mario Dejung 14 Nov '13

14 Nov '13

Hi Andreas, have you tried copy/paste the character from somewhere, for example Terminal, to the command line? I have “the same” problem with German keyboard layout. I am not able to type the ~ character within the command line of Chimera… But with copy paste, the character is visible and it works… Not a good workaround… by the way… Mario

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Speed problems under Mavericks
by Mario Dejung 14 Nov '13

14 Nov '13

I found Tom Goddard's post about the Mavericks bug and the change on the daily build with the disabled advanced graphics. So I am not sure, if my problem is related to the crashing of chimera. My problem is the speed of chimera under Mavericks. I work with molecules of about 20000 Atoms and rotating a PDB of this size is very painful. I didn’t had problems with Lion. I am wondering now, if I am the only person with speed problems under Mavericks, or if other people have similar issues. Is there a way to improve the speed of chimera under Mavericks? Kind regards Mario

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Re: [Chimera-users] Using runCommand outputs
by Tom Goddard 14 Nov '13

14 Nov '13

Hi Ahir, Every Chimera command has an equivalent Python function. I just didn't tell you all the places you would have to look to find them. Commands that have a separate dialog (graphical user interface) usually have their own code directory and are not in Midas/__init__.py. So for example the findclash command has the equivalent Python function "detectClash()" in directory chimera/share/DetectClash (On Mac the directory is Chimera.app/Contents/Resources/share/DetectClash). So it can be a bit tricky to find the Python. Here's what I do when I can't find the Python code. Each command is registered in Chimera code with the routine addCommand(). So I search for addCommand in all the share directories. Below is a list for Chimera 1.8. You are right that trying to save reply log output instead of directly running Python functions is not feasible for more complex scripts. Tom $ cd Chimera-1.8.app/Contents/Resources/share $ grep "addCommand(" */*.py Accelerators/ChimeraExtension.py:addCommand('ac', accel_cmd, None, help = True, changesDisplay = True) AddAttr/ChimeraExtension.py:addCommand("defattr", cmdAddAttr, help=True, changesDisplay=False) AddCharge/ChimeraExtension.py:addCommand("addcharge", cmdAddCharge, help=True, changesDisplay=False) AddH/ChimeraExtension.py:addCommand("addh", cmdAddH, help=True) Addions/ChimeraExtension.py:addCommand("adions", cmdAddions, help=True) Animate/ChimeraExtension.py:# addCommand(command, cmdFunc, revFunc=None, help=None, changesDisplay=True) Animate/ChimeraExtension.py:addCommand('scene', Animate/ChimeraExtension.py:#addCommand('transition', Animate/ChimeraExtension.py:#addCommand('animate', Animate/ChimeraExtension.py:addCommand('kfadd', Animate/ChimeraExtension.py:addCommand('kfclear', Animate/ChimeraExtension.py:addCommand('kfdel', Animate/ChimeraExtension.py:addCommand('kfmove', Animate/ChimeraExtension.py:addCommand('kfmovie', Animate/ChimeraExtension.py:addCommand('kfsave', Animate/ChimeraExtension.py:addCommand('kfshow', Animate/ChimeraExtension.py:addCommand('kfstatus', Animate/ChimeraExtension.py:addCommand('kftrans', Aniso/ChimeraExtension.py:addCommand("aniso", cmdAniso, revFunc=cmdUnaniso, help=True) BuildStructure/ChimeraExtension.py:addCommand("invert", cmdInvert, help=True) ChangeChainIDs/ChimeraExtension.py:addCommand("changechains", cmdChangeChains, help=True, changesDisplay=False) Combine/ChimeraExtension.py:addCommand("combine", cmdCombine, help=True) CrystalContacts/ChimeraExtension.py:addCommand('crystalcontacts', crystal_contacts_command, help = True) DetectClash/ChimeraExtension.py:addCommand("findclash", cmdDetectClash, revFunc=cmdUndetectClash, help=True) ESP/ChimeraExtension.py:addCommand("coulombic", wrapper, help=True) EnsembleMatch/ChimeraExtension.py:addCommand('tile', tile_cmd, tile_cmd, help = True) EnsembleMatch/ChimeraExtension.py:addCommand('cluster', cluster_cmd, None, help = True) FindHBond/ChimeraExtension.py:addCommand("hbonds", cmdHBonds, revFunc=cmdUnHBonds, help=True) FindHBond/ChimeraExtension.py:addCommand("findhbond", cmdHBonds, revFunc=cmdUnHBonds, help=True) FitMap/ChimeraExtension.py:mt.addCommand('fitmap', fit_map, unfit_map, help = True) Fly/ChimeraExtension.py:addCommand('fly', fly_cmd, help = True) IcosahedralCage/ChimeraExtension.py:Midas.midas_text.addCommand('hkcage', hkcage, help = True) Ilabel/ChimeraExtension.py:addCommand("2dlabels", doLabel2DCmd, help=True) Intersurf/ChimeraExtension.py:midas_text.addCommand("intersurf", emo.commandLine) Lighting/ChimeraExtension.py:addCommand('lighting', lighting, help=True) ListInfo/ChimeraExtension.py:addCommand("list", emo.command, help=True, changesDisplay=False) ListInfo/ChimeraExtension.py:addCommand("listmodels", emo.command, help=True, changesDisplay=False) ListInfo/ChimeraExtension.py:addCommand("listchains", emo.command, help=True, changesDisplay=False) ListInfo/ChimeraExtension.py:addCommand("listresidues", emo.command, help=True, changesDisplay=False) ListInfo/ChimeraExtension.py:addCommand("listatoms", emo.command, help=True, changesDisplay=False) ListInfo/ChimeraExtension.py:addCommand("listselection", emo.command, help=True, changesDisplay=False) ListInfo/ChimeraExtension.py:addCommand("listphysicalchains", emo.command, help=True, changesDisplay=False) ListInfo/ChimeraExtension.py:addCommand("listen", emo.command, help=True, changesDisplay=False) ListInfo/ChimeraExtension.py:addCommand("sequence", emo.command, help=True, changesDisplay=False) MMMD/ChimeraExtension.py:addCommand("minimize", emo.cmdMMMD, help=True) MMMD/ChimeraExtension.py:#addCommand("dynamics", emo.cmdMMMD, help=True) Mask/ChimeraExtension.py:Midas.midas_text.addCommand('mask', mask_cmd, help = True) MatchMaker/ChimeraExtension.py:addCommand("mmaker", cmdMatchMaker, help=True) MatchMaker/ChimeraExtension.py:addCommand("matchmaker", cmdMatchMaker, help=True) Measure/ChimeraExtension.py:addCommand('measure', measure_cmd, help = True) MeshToMolecule/ChimeraExtension.py:addCommand('meshmol', mesh_to_molecule, help = True) Midas/midas_text.py:def addCommand(command, cmdFunc, revFunc=None, help=None, changesDisplay=True): ModelClip/ChimeraExtension.py:addCommand('mclip', mclip_command, unclip_command, help = True) MoleculeCopy/ChimeraExtension.py:addCommand('mcopy', mcopy_cmd, help = True) MoleculeMap/ChimeraExtension.py:addCommand('molmap', molmap_cmd, help = True) Morph/ChimeraExtension.py:addCommand("morph", emo.cmdMorph, help=True) Movie/ChimeraExtension.py:addCommand('coordset', coordset, help = True) MovieRecorder/ChimeraExtension.py:addCommand("movie", doMovieCmd, help=True, changesDisplay=False) MultiscaleColor/ChimeraExtension.py:Midas.midas_text.addCommand('msc', msc_command, msc_undo_command, help = True) NucleicAcids/ChimeraExtension.py:addCommand('nucleotides', nucleotides, revFunc=unnucleotides, help=True) Play/ChimeraExtension.py:addCommand('play', play, reverse_play, help = ('play.html', 'Play')) RNALayout/ChimeraExtension.py:addCommand('rna', rna_cmd, help = True) Ramachandran/ChimeraExtension.py:addCommand("ramachandran", emo.cmdLine, help=True) ResRenumber/ChimeraExtension.py:addCommand("resrenumber", cmdResRenumber, help=True, changesDisplay=False) Rotamers/ChimeraExtension.py:addCommand("swapaa", cmdRotamers, help=True) Segger/ChimeraExtension.py:Midas.midas_text.addCommand('segment', segment, None, help = True) Shape/ChimeraExtension.py:addCommand('shape', shape_cmd, help = True) Solvate/ChimeraExtension.py:addCommand("solvate", cmdSolvate, help=True) SplitMolecule/ChimeraExtension.py:Midas.midas_text.addCommand('split', split_molecules, help = True, changesDisplay=False) StructureDiagram/ChimeraExtension.py:addCommand("struct2d", emo.cmdLine, help=True, changesDisplay=False) Surface/ChimeraExtension.py:addCommand('sop', sop_cmd, unsop_cmd, help = True) SurfaceColor/ChimeraExtension.py:addCommand('scolor', scolor_cmd, scolor_cmd, help = True) SurfaceColor/ChimeraExtension.py:addCommand('scolour', scolor_cmd, scolor_cmd, help = True) SurfaceZone/ChimeraExtension.py:Midas.midas_text.addCommand('bondzone', bzone, no_bzone, help = True, changesDisplay=False) SymmetryCopies/ChimeraExtension.py:Midas.midas_text.addCommand('sym', symmetry_copies, undo_symmetry_copies, Topography/ChimeraExtension.py:addCommand('topography', topo, help = True) ViewDock/ChimeraExtension.py:addCommand("viewdock", emo.cmdViewdock, help=True) VolumeFilter/ChimeraExtension.py:addCommand('vop', vop_cmd, help = True) VolumeSeries/ChimeraExtension.py:addCommand('vseries', vseries_cmd, help = True) VolumeViewer/ChimeraExtension.py:addCommand('volume', volume_cmd, help = True) Zone/ChimeraExtension.py:Midas.midas_text.addCommand('zonesel', zone_cmd, help = True) apbs/ChimeraExtension.py:addCommand("apbs", emo.cmdLine, help=True) blastpdb/ChimeraExtension.py:addCommand("blast", emo.cmdLine, help=True, changesDisplay=False) blastpdb/ChimeraExtension.py:addCommand("psiblast", emo.cmdLine, help=True, changesDisplay=False) chimera/writeSel.py:addCommand("writesel", midasCmd, help=True) pdb2pqr/ChimeraExtension.py:addCommand("pdb2pqr", emo.cmdLine, help=True) vina/ChimeraExtension.py:addCommand("vina", vinaEmo.cmdLine, help=True) $ On Nov 14, 2013, at 1:21 AM, wrote: > Thanks for the prompt reply Tom, that explains things! I took a look at the init.py file, and I can see that it's not as straight forward and as you said, some runcommand functionality is not represented by midas commands too right? For example, I cant find findclash for example. I am not beyond using runcommand ("findclash" blah blah log/savefile True) etc, but what is the easiest way to feed the output of runcommand that does not have a savefile option , i.e if the ouput goes not to the reply log but rather to IDLE, is there any way of getting this data back to a file, without manually cut and pasting it into a file and saving it? Because the saveReplyLog from tkgui does not save anything if I am running IDLE, because the output goes to IDLE (and I am using IDLE during writing/testing the script). If there is a way of doing this, then its a suitabe workaround for me! > > Thanks again > Ahir > > One thing, > > Quoting Tom Goddard > >> Hi Ahir, >> >> Unfortunately runCommand() does not return any Python objects resulting from the command -- would be convenient if it worked that way. If you want return values from a command you need to call the Python function that does that command. Most of those are in file >> >> chimera/share/Midas/__init__.py >> >> with the function name matching the command name, e.g. rmsd() for the "rmsd" command, or match() for the "match" command. So open that file in a text editor and search for the command you want. We unfortunately don't have documentation on the Python functions so this can be troublesome and I'm sure is why you prefer runCommand(). We will provide documentation for all the Python functions in our next generation Chimera that we are working on now. >> >> Tom >> >> >> On Nov 13, 2013, at 8:40 AM, wrote: >> >>> Hello all, I am getting confused by the runCommand() functionality when I am trying to run scripts. When I run my python script through IDLE(From Tools-General), the ouput of runcommand commands like rmsd etc are given the IDLE. I want to store the output from runcommand into a variable dynamically. I dont want to save from the ReplyLog (by running program without IDLE) or output to file, is there something in python itself that I am not understanding and hence, not using, or is it not possible to store the output of runcommand into a variable/list etc, as it is possible for the midas.rmsd function for example. I only ask because I prefer to use the command line functionality over the midas command. If it is only possible with the direct midas, how do I find out the equivalent command of the runcommand for the midas python formatting? >>> >>> Thank you >>> Sorry if my question is a bit confusing! >>> >>> Ahir >>> >>> ---------------------------------------------------------------- >>> This message was sent using IMP, the Internet Messaging Program. >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> >> > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. >

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Query related to chimera downloading
by akhilesh verma 14 Nov '13

14 Nov '13

Dear Sir/Madam, I am a research scholar from Cachar Cancer Hospital, India. I tried to download Chimera V-1.8.1. but could not download. It is showing insufficient permission. Kindly tell me how to set up this problem. Thanking you n anticipation -- Yours sincerely, *Dr. Akalesh Kumar Verma* *Post-Doc Research Associate* *Department of Molecular Oncology* *Cachar Cancer Hospital & Research Centre* *Mobile : +91-8471956679* *____________* *Personal Disclaimer:--* *Any information contained in this e-mail and/or any attachments is confidential and only intended for reception and use by the specified person. If you are not the intended recipient, please return the email to the sender and delete it afterwards. In this case any copying, forwarding, printing, disclosure and use is strictly prohibited.* *_____________________________*

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chimera multiple sequence alignment
by Covell, David (NIH/NCI) [E] 13 Nov '13

13 Nov '13

Dear Chimera Help, I have used NCBI's COBALT to align the active site residues for the ~400 kinases in the 'kinome tree'. This fasta alignment can be exported and read into chimera. Once loaded, tools > sequence > multialign/viewer > info > percent identity gives me the % identity for a pair of sequences. Since I have ~400 sequences, I would like to know whether the upper-triangular matrix of percent identities can be done automatically. If so, can a weight matrix for scoring (BLOSUM62) be used? Thanks in advance for your help. David Covell, Ph.D.

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Issues with characters on command line (OS X 10.9)
by Andreas Göransson 13 Nov '13

13 Nov '13

Hi everybody! I am experiencing a strange issue with the command line. I have OS X 10.9 and Chimera 1.8.1. I can't type tilde sign (~) in the command line - nothing comes up. Other Alt-combinations to produce special characters as @ works fine. Have any of you the same problem / any suggestions for solution? Thanks, Andreas

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Using runCommand outputs
by a.pushpanath＠mail.cryst.bbk.ac.uk 13 Nov '13

13 Nov '13

Hello all, I am getting confused by the runCommand() functionality when I am trying to run scripts. When I run my python script through IDLE(From Tools-General), the ouput of runcommand commands like rmsd etc are given the IDLE. I want to store the output from runcommand into a variable dynamically. I dont want to save from the ReplyLog (by running program without IDLE) or output to file, is there something in python itself that I am not understanding and hence, not using, or is it not possible to store the output of runcommand into a variable/list etc, as it is possible for the midas.rmsd function for example. I only ask because I prefer to use the command line functionality over the midas command. If it is only possible with the direct midas, how do I find out the equivalent command of the runcommand for the midas python formatting? Thank you Sorry if my question is a bit confusing! Ahir ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Mapping Change in Surface Exposed Residues on Model
by Joshua Carter 12 Nov '13

12 Nov '13

Hello, My name is Josh Carter and I am an undergraduate at MSU working on some modeling. I am working in particular on a ribo-nucleo-protein complex that undergoes a conformational change upon target binding. I am trying to find a good way to map the change in surface exposed residues after this conformational change occurs. I have a morph model of the two states and was just wondering if there was a way to map using chimera which models are surface exposed or not? Thanks, Josh

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Re: [Chimera-users] set attribute coil/helix/sheet in chimera
by Tom Goddard 12 Nov '13

12 Nov '13

There is no isCoil attribute. If a residue is not helix and not sheet then it is coil. So to set residues 106-121 to coil use setattr r isHelix 0 :106-121 setattr r isSheet 0 :106-121 Tom On Nov 11, 2013, at 3:58 AM, Puey Ounjai wrote: > Dear Tom, > > I am wondering if there is any way to set attribute to coil for particular residue just for rendition? > I tried command "setattr" it works perfectly for helices and sheet but I dont know if option isCoil do exist > > Thanks, > Puey

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suggestion: stereo3D
by Dougherty, Matthew T 12 Nov '13

12 Nov '13

Hi, I would recommend an option to lock the focal plane to the min clipping plane. having that track will make first pass stereography easier to create the stereo3D parallax budget. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Automatic mutations
by James Starlight 12 Nov '13

12 Nov '13

Dear Chimera users! I'm looking for the possible python script which using the Chimera's source would introduce selected mutations in the defined PDB file and produce PDB output containing such protein with the selected substitution residues. It would be also good if rotamers for mutation residues would be backbone dependent or taken from the existing rotamer libraries (although its not essence because I can run minimization on the mutants) Previously I've done such tasks with selectivity mutations via Chimera-GUI rotamer plugin but now I'd like to obtain big series of the mutant of studied protein for further examinations of such mutants by means of molecular dynamics simulation. Could someone provide me with such script if it could not be very complicated to make it? Thanks for help, James

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Re: [Chimera-users] Problems with binding site representation
by Elaine Meng 12 Nov '13

12 Nov '13

Hi Vigneshwari, The CASTp approach is great in that it automatically figures out for you where the pocket boundaries are (where the pocket ends and the outside begins), and provides volume and other measurements. CASTp works with apo structures as well as liganded. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/castp.html> <http://sts-fw.bioengr.uic.edu/castp/calculation.php> Another tool that can be used with Chimera is the Voss Volume Voxelator (3V) web server, which will create "density"-type maps of the pockets and tunnels in a structure. In Chimera, you can open the resulting map, adjust the isosurface level as desired in Volume Viewer, then measure the volume enclosed in the isosurface with the "Measure and Color Blobs" tool (in menu under Tools… Volume Data). <http://3vee.molmovdb.org/> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/fram…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pickblo…> These do not display different inside and outside colors, but they use other ways to locate the pocket boundaries. The complicated procedure in Chimera to generate the pockets with different inside and outside coloring is because we currently don't have 2-sided coloring on a single surface. The map from 3V could be shown with two different isosurfaces slightly offset from each other in two differen colors, but I don't know how useful that would be. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/fram…> You may need to use a different program if none of the above suffice. Best, 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 Nov 11, 2013, at 11:14 PM, vigneshwari subramanian <vignesh.bioinfo(a)gmail.com> wrote: > Hi Elaine, > Thanks for your email. > > Our aim is to show the differences in the volume of binding cavities when an agonist and antagonist binds. We also want to show the ligand free state of the cavity. The reason for having 2 different colors is to clearly see if the volume marks the inner or outer surface of the cavity. > > Since this doesn't work very well, I thought I could solvate the cavity and display that surface. I am not sure if there better ways to represent the volumes of binding cavities. > > regards, > vigneshwari >

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Re: [Chimera-users] Problems with binding site representation
by Elaine Meng 11 Nov '13

11 Nov '13

Hi Vigneshwari, You can see the manual page by using command "help measure" or you can see it on our website here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#contact…> Best, 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 Nov 9, 2013, at 3:31 AM, vigneshwari subramanian wrote: > Hi Elaine, > > Thank you so much for your timely help. I could actually make the same figure. I need to do the same for our dataset. > > It would be really helpful if you can tell me what each of these parameters mean. I think you gave an overview. But I would like to know what each of these mean. > > 3 slab -.1,0 > > measure contactArea #0.2 #0.1 3 slab -.1,0 color tan > measure contactArea #0.2 #0.1 2.99 slab -.11,-.01 color cornflowerblue > > I checked the manual. But I couldn't find any information about measure contactArea. > > I am there in the chimera list. > > regards, > vigneshwari

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Change line width of stick representation?
by Amy Davenport Migliori 09 Nov '13

09 Nov '13

Does anyone know if it is possible to change the line width of stick representations? Either that or add the ability to have depth in wire representations (i.e. shading, etc)? I would greatly appreciate any help. Thanks Amy Migliori, UCSD

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Problems with binding site representation
by vigneshwari subramanian 08 Nov '13

08 Nov '13

Dear all, I have been trying hard to make a figure similar to the one shown in this web page. http://www.cgl.ucsf.edu/chimera/ImageGallery/ I would like to have 2 different colours to represent the inner and outer surfaces of binding site. I opened 2 different structures of the same protein and adjusted the surface parameters (probe radius and vertex density) . But that doesn't seem to work. I would be really happy if someone can help me to sort out this issue. thanks, vigneshwari

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Group cylinder with a PDB and fit together
by Mario Dejung 07 Nov '13

07 Nov '13

Hi all, I created a some cylinders in chimera to visualise the symmetry axis and the rotation center of a hexametric structure. Is there a way to fix the position of these cylinders relative to the pdb structure? So when I fit the structure, the cylinders will also rotate in the same way. And, by the way, is it possible to duplicate these cylinders, or do I have to create a .bild file and import it several times? Thanks for your feedback. Mario

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How to change the default color for pseudobonds?
by Oliver Clarke 06 Nov '13

06 Nov '13

Greetings, Is there any way to change the default color for pseudo bonds (e.g. distance monitors)? I generally work on a white background, and the default of yellow is very difficult to see. Pretty much everything else in the Chimera GUI seems to be customizable, which I love, but I can’t see how to alter the default in this particular instance. Many thanks, Oliver.

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Specifc silouhettes
by m.maletta＠nki.nl 05 Nov '13

05 Nov '13

Dear All I have docked an X-ray model inside an EM density (mrc). I would like to visualize the density (mrc) with the silhouettes option on and pdb file with the silhouettes option off. Is this possible? Best Max __________________________________ Massimiliano Maletta post-doc in NKI Netherlands Cancer Institute -Antoni van Leeuwenhoek Hospital Plesmanlaan 121 B6 1066CX Amsterdam group of Peter Peters www.nki.nl/research/peters/ | www.necen.nl m.maletta(a)nki.nl Tel : +31 20 512 2022 Fax : +31 20 512 2029

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chimera scalability on irix
by tyrrell t 04 Nov '13

04 Nov '13

I couldn't find any information on the subject, and have no hardware to test at the moment, but for a future deployment I need to work with IRIX systems, and I was wondering if chimera is coded to take advantage of multiple MIPS CPUs, or is it strictly a CPU-bound application? ie: would it run better on a dual-cpu octane system at 600mhz, or a 700mhz uni-processor fuel system? ( or something along this line )

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calculate axes from centroids
by Elaine Meng 04 Nov '13

04 Nov '13

On Nov 3, 2013, at 7:49 PM, Lili Peng <lilipeng(a)gmail.com> wrote: > Hi Elaine, > I've inquired you in the past regarding defining angles and planes in UCSF Chimera. > Do you know if there's a way to define an axis through two centroids, or through the center-of-mass of a residue and the centroid of a subunit, some combination like that? > Thank you, > Lili > Hi Lili, Currently, axes (and planes and centroids) can only be calculated from sets of atoms, not centroids. However, it can done in current Chimera by defining centroids, adding fake atoms at their positions, and using those atoms to define axes. You can specify whether each centroid calculation is mass-weighted (center of mass) or not (default, center of geometry). (a) use Axes/Planes/Centroids (or command "define") to define the desired centroids (b) look in Reply Log for the coordinates of each centroid ( c) add atoms: Tools… Structure Editing… Build Structure, Start Structure section, use settings to add atom with specific x,y,z coordinates to the existing model (the one whose atoms you used to define centroid) (d) use new atoms to define axis <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/str…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> There is also a "measure center" command that will automatically create a fake atom (option "mark true"), so you could use that instead for steps a-c, but it always does mass-weighting. For non-mass-weighted centroids, you would need to use the full process outlined above. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center> I hope this helps. Sorry it is not as simple as it should be. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Fitting models into density - meaning of values
by Jessica Holien 30 Oct '13

30 Oct '13

I have been using Chimera to fit some homology models into the EM density (23A resolution) of a large complex. Although by eye it looks good I am trying to work out if statistically it is good. Can anyone tell me what is a good "Average Map Value" and what is a bad one? Thanks

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Coloring distance lines between atoms
by Tom Goddard 30 Oct '13

30 Oct '13

Hi Damien, Here is a Chimera Python script colordist.py that lets you color distance lines between atoms based on how long the distance is. The colors update as you move one model relative to another. After showing some distances, for instance with the "distance" command you would use command runscript colordist.py 8.5 green red to color the distance lines less than 8.5 Angstroms green, and longer ones red. The script needs to be in the directory you started Chimera in (e.g. on Linux), or you can specify a full path to the script "runscript /Users/Smith/colordist.py …", or use the Chimera "cd" command to change to the directory containing the script. You can select specific distance lines to color with the mouse and use runscript colordist.py 8.5 green red sel You can stop the color updating using runscript colordist.py or for just selected distance lines runscript colordist.py sel Tom On Oct 24, 2013, at 3:13 AM, Damien Larivière wrote: > Hi Tom, > > So, here is a reminder for the script we talked about. > > The idea is as follows: > > Once I have loaded several proteins in Chimera, once I have calculated distances between residue pairs that are displayed in the distance popup window, once I have displayed visually the distance as a colored stick pseudobond, then I would like a switch of the pseudobond color to occur when the distance is higher than a given value as I'm moving the proteins. > So, in my current manual modeling, I'm calculating a total of 24 distances between 5 proteins, I ask Chimera to display 24 pseudobond, most of them are initially let'say red, I load the script after having editing it with the distances and the associated maximal values, I move the proteins and the pseudobond color turn from red to yellow when the distance get lower than the maximal value defined for this distance in the script. And inversely, a pseudobond turns to red from yellow when it gets higher than a maximum distance. > > Let me know if you need more explanations. > > Many thanks for your help, > > Damien >

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color a small molecule in a .mol2 file by red to blue gradient of the partial charges
by Francois Berenger 30 Oct '13

30 Oct '13

Is it possible to do this in Chimera? I'd like a white background too. Thanks a lot, F.

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how to make the background of Chimera-generated images transparent
by Gea-Ny Tseng/FS/VCU 30 Oct '13

30 Oct '13

Dear Chimera developers and users: I would like to know how to make the background of Chimera-generated images transparent. I used to be able to do this with an older version of Chimera. But with Chimera 1.8, I could not figure out how to do this. There are options in the 'Color/Background' to adjust 'Opacity', which to me means that I could make the background transparent by using 'zero'. But this did not happen. Could you please advise? Thank you. Gea-Ny Tseng, PhD Dept of Physiology & Biophysics Virginia Commonwealth University

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Symmetry generation question
by Bala subramanian 29 Oct '13

29 Oct '13

Hello, 1) I have modelled one chain of a multimer. Since this is a modelled structure I dnt have any symmetry information in my pdb. In such case, how can I generate the symmetry related copies. Say I want to apply a fivefold symmetry along z-axis, how can I achieve it ? 2) I used a template structure from PDB to model my structure. What is the correct way to apply the symmetry of existing pdb model to my modeled chain. I tried this as follows, I opened my model as #0 and then the template pdb structure #1 and tried the following sym command and obtained an error as '#0 has no biological unit info.' sym #0 #1 Thanks, Bala -- C. Balasubramanian

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coloring plane by ESP
by Elaine Meng 29 Oct '13

29 Oct '13

Hi Marek, Just thought I'd mention that in Chimera you can color a plane that is in any orientation by the values in an ESP map. Unfortunately it doesn't work with the planes from Axes/Planes/Centroids, but you can create a rectangular plane with specified height and width with command "shape rectangle". Then you can open the molecule and the ESP map, activate/deactivate models (freeze/unfreeze them) and use the mouse to position the rectangle however you like in relationship to the molecule. Then you can use the "Surface Color" tool (aka Electrostatic Surface Coloring) to color the rectangle by the ESP map values. If you didn't already have an ESP map, you could use the PQR and APBS tools in Chimera to calculate one with APBS, or use the Coulombic Surface Coloring tool with option to "Compute grid" (i.e. make ESP map). Attached image is for 3eeb chain B, ESP map file 3eebB.phi ( available from link near bottom of the Surface Properties image tutorial <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> ), and rectangle created with command: shape rectangle height 50 width 50 widthdiv 100 heightdiv 100 center protein It shows the area of strong positive potential near where the highly negatively charged ligand binds. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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no moleculr dispay with version 1.8
by Robert Wohlhueter 28 Oct '13

28 Oct '13

I have chimera-1.5.3 running on my Linux-AMD64 Ubuntu (12.10) computer. It works fine in every respect. Recently I installed version 1.8, with runs, but with one fatal flaw. By "runs", I mean the chimera screen comes up, the menus display. If I load (say, a pdb file), it seems to be there in the sense, for example, that I can open and view its sequence. BUT the molecule display window is absolutely blank (black). I suspect it has either to do with my python installation, or with my NVIDIA graphics driver. But whatever the problem, it effects only v. 1.8, not v. 1.5.3. For NVIDIA driver I'm using version 310.14. For python, I understand chimera uses 2.7. My python executable is indeed set as version 2.7.3 (that is, `python --version1 returns 2.7.3), though I have version 3 installed, and it could be used, if needed. I'm not all so clear on how envars PYTHONHOME and PYTHONPATH may or may not effect chimera. Of course, the easy way out is to stick with chimera-1.5.3 -- but one likes to stay up-to-date. Thanks in advance for any profound wisdom. Bob Wohlhueter

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Need help with fit into segment function
by Michael Matho 28 Oct '13

28 Oct '13

Hello, I have an EM map segmented in 5 segments I need to fit 5 molecules into. I'm trying to select a specific segment in order to fit each molecule individually, one after the other. After reading the tutorial, I still cannot figure out how to select only one segment of the map: If I try selecting from "Render/select by attribute" and choose "Segmentation regions" (and I do have the 5 segments ready), only the full map shows up, not the segments! In the "fit to segment" window, I select the molecule to fit and click on Fit... then there's a bug. I'd appreciate your help on how to finalize my fit. Thanks, Michael H. Matho, Ph.D. | Research Associate | Department of Cell Biology La Jolla Institute for Allergy and Immunology 9420 Athena Circle | La Jolla, CA, 92037 Tel: (858) 752-6631 | mmatho(a)liai.org

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Morph movie issue
by Kang, Yanyong 28 Oct '13

28 Oct '13

Dear Chimera developer, I have some problem for making morph movie. My start model has the secondary structure, but the final model loses most of the secondary structure. My morph movie could not show the secondary structure transition of the protein structure. If I change final model as the start model, the start model is as the final model. Secondary structure is the same with the start model. Do you have any ideas to solve this issue? Thank you very much Best, Yanyong Dr. Yanyong Kang Laboratory of Structural Sciences Van Andel Research Institute Tel, 616-234-5446

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rotation of the molecule using plane and the axis ?
by Marek Maly 25 Oct '13

25 Oct '13

Hello, if I define plane "p" using 3 atoms of the given molecule, is there any possibility to rotate consequently molecule into the position in which the chosen axis of the coordinate system (x or y or z) is perpendicular to the plane "p" ? (Of course except slow and not accurate "manual" rotation by mouse). Than you, Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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can get sequence from UniProt website
by Elaine Meng 25 Oct '13

25 Oct '13

Hi Pavithra, I forgot to mention that you could just go to the UniProt web site and save the sequence as a file, then open the file in Chimera. For example, I went to UniProt, searched for oprd_human, then in the Sequences section of the oprd_human page, clicked "FASTA" to get to the URL below, contents of which you can save as plain text file named ending in .fa or .fasta and then open in Chimera with File... Open. <http://www.uniprot.org/uniprot/P41143.fasta> It would not have the annotations mentioned in the comparative modeling tutorial, but those aren't important for doing the tutorial. After opening the FAST file as described above, you can then carry on with the tutorial starting with the fourth paragraph in the "Blast Search for Templates" section ("The next step...". <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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chimera in mac osx 10.9
by Pu Qian 25 Oct '13

25 Oct '13

Hi, I upgraded my mac to 10.9 Marvericks. Chimera does not show up input text in Command windows or other text windows properly. I'm using version 1.9, 2013-10-24, 64-bit for mac OSX. It would be a great appreciated if you could tell me which version I should use for this new OSX. Thanks. Best regards Pu Qian The University of Sheffield, UK

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BadStatusLine error
by Pavithra 24 Oct '13

24 Oct '13

Dear chimera users, I'm trying comparative modeling tutorial in chimera tutorials and I'm getting the following error in using fetch uniprot id. *Steps followed: * Menu--> fetch by ID--> selected uniprot--> "oprd_human" "P41143" (tried all combinations) *Error:* *BadStatusLine: '' File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 371, in _read_status raise BadStatusLine(line) See reply log for Python traceback. * I tried changing the preference to use "http" but nothing fix it. please help. -- regards, Pavithra.K.B.

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Typing broken in Mac Mavericks (10.9) with 64-bit Chimera
by Tom Goddard 24 Oct '13

24 Oct '13

With the new Mac operating system Mavericks (Mac OS 10.9), typing into Chimera entry fields is not working in 64-bit Chimera but works correctly in 32-bit Chimera. Also as reported earlier a Mavericks graphics driver bug causes Chimera 1.8 to crash displaying any atoms or bonds. The crashing problem has been fixed in today's Chimera daily build (by disabling an advanced graphics feature automatically on Mac 10.9). So the only Mac Chimera that will work correctly on Mavericks is today's 32-bit daily build (or newer). Tom

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odd surface graphics artifact
by Scott Classen 23 Oct '13

23 Oct '13

Hello, I'm trying to fade a surface to 100 transparent with the following command transparency 100,s #2 frames 30; wait 30 and when the surface goes from 0% transparent to 1% transparent I see the following clipping at the top of the surface: What is causing this and how can I eliminate it? Thanks, Scott

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Chimera crashes on Mac OS 10.9 Mavericks
by Tom Goddard 23 Oct '13

23 Oct '13

For those updating to the newly released Mac operating system Mavericks (10.9), we already have several reports that Chimera crashes showing any molecule due to a graphics driver bug in the new Mac operating system. I suggest not updating to Mavericks immediately if you want Chimera to continue to work. Only Apple can fix this bug. But we will disable the advanced graphics that leads to the crash in tonight's daily build. So if you already updated to Mavericks you can try the Chimera daily build (available about 16 hours after this post) instead of the Chimera 1.8 release. If you want the Chimera 1.8 release to work in Mavericks you'll need to disable DrawElementsInstanced in the Chimera debug graphics driver dialog. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html Disabling this graphics feature (which is what the daily build will do automatically) will cause rendering of large molecules to be slower when atoms are shown as spheres/balls or bonds are shown as cylinders, about 30 times slower. Still it should be as fast as the older Chimera 1.6 version where we did not use this advanced graphics feature at all. Tom

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Problem with Chimera-1.8-linux-x86_64
by Stephen P. Molnar 23 Oct '13

23 Oct '13

I have installed chimera-1.8-linux-x86_64 in VMware Player v-6.0.0 build-1295980 without any waning or error messages. When I start chimera I get the splash screen, then: ./chimera X Error of failed request: BadDrawable (invalid Pixmap or Window parameter) Major opcode of failed request: 72 (X_PutImage) Resource id in failed request: 0x4000064 Serial number of failed request: 1352 Current serial number in output stream: 1358 computation@inga:~/Apps/chimera/bin$ Please advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate www.FoundationForChemisry.com (614)312-7528(c) Skype: smolnar1

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Chimera and Mac Mavericks
by Evan Kantrowitz 23 Oct '13

23 Oct '13

I just install Mavericks on my Mac. Chimera starts OK, but if you try to type into a field, like the PDB fetch field, entering key strokes is very hard. Evan ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu<mailto:evan.kantrowitz@bc.edu> Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow<http://www2.bc.edu/~kantrow> Chestnut Hill, MA 02467 -------------------------------------------------------------------

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hydrophopic interaction
by LU Zen 23 Oct '13

23 Oct '13

Hi All, I have a amphipathic helix/membrane complex assembled with CHARMN-GUI and I'll like to show those residues that come into contact with the lipid bilayer. Using find clash/contact function, I can see many lines joining the atoms of both the residues and lipid bilayer. However, I don't really know how to pick the true hydrophopic interaction from the rest of the clashes/contacts. In addition, is there a way to quatify which these interactions may be tighter than the other. Any suggestion is appreciated. Thanks, ZL -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Create a protein model using Chimera?
by Maja Divjak 19 Oct '13

19 Oct '13

Hello Chimera, I have looked high and low for the propeptide domain of IL-1 beta, but it does not exist as a PDB. I was therefore wondering what is the best approach to generating a 3d structure for the propeptide domain using the protein sequence and Chimera? If you could please outline a possible process, I would very much appreciate it. I see you have tutorials for comparative modeling, but in this case there is nothing to compare it to except other homologous sequences from the IL-1 family. I look forward to your reply! Thank you and best wishes, Dr Maja Divjak, WEHI, Melbourne, Australia ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________

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