- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Chimera STL files
by Tom Goddard 20 Nov '13

20 Nov '13

Hi Julian, The problem is that you create a large density map for your protein, but then Chimera doesn't display it at full resolution, because it is so large. To make Chimera display the contour surface of the full resolution map set the "Step" value in the volume viewer dialog to 1, or use the equivalent command "volume #0 step 1" after the molmap command. Making the grid spacing 0.1 (40 times smaller than the resolution of 4 Angstroms) is likely to create a huge STL file that the printer will have trouble with, and it won't give any smoother appearance than say 0.4 I think. Tom On Nov 20, 2013, at 7:54 AM, Julian Gough wrote: > Dear Tom, > > I read what you wrote here: > > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-May/008825.html > > I am really struggling to make an STL file for a coiled coil protein for 3D printing. What I see happening in Chimera does not seem to correspond to what you say, i.e. I use "molmap #0 4 grid 0.1" which according to you should be super-smooth -being far beyond what you suggest-, but the STL file that I export still has very large and obvious triangles. > > I have played with it a great deal and I cannot find any way to control the number of triangles in the STL file. Whatever parameter I use for the grid, the output file is roughly similar in size. I can certainly fill the memory and crash it by making the grid smaller, but this is not reflected in the exported STL file. > > ANy guidance much appreciated. > > Julian > > > -- > ~~~~~~~~~~~~~~~~ > Julian Gough > Professor of Bioinformatics > University of Bristol > Department of Computer Science > Merchant Venturers building > Woodland rd, Bristol, UK, BS8 1UB > Tel: +44 (0)117 3315221 > Web: http://bioinformatics.bris.ac.uk > <owen2.py><owen2.stl>

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Set interatomic distances
by George Patargias 18 Nov '13

18 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 18 Nov '13

18 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 08 Nov '13

08 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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