- 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

2 2

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

2 2

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

2 2

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

2 1

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.

3 3

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

3 2

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 )

2 1

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

1 0

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

2 3

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 >

1 0

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.

2 2

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

2 1

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

2 1

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

1 0

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

3 2

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

2 3

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

2 1

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/

2 1

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

1 0

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

1 1

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.

3 4

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

1 0

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

3 2

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

1 0

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

2 1

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 -------------------------------------------------------------------

2 1

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.

2 1

Create a protein model using Chimera?
by Maja Divjak 18 Oct '13

18 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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Re: [Chimera-users] Cross-section question
by Tom Goddard 18 Oct '13

18 Oct '13

Hi Lawrence, Sure it is easy to see plane 72. Use the Volume Viewer dialog, show the planes panel (menu Features / Planes), press the "One" plane button in that panel and set the plane number entry field to 72. To assure you see the full resolution data make sure "Step" is set to 1 above the volume dialog density map histogram, and that "depth" is set to 1 in the Planes panel. This and other Chimera density map features are described in the Chimera guide to volume data display http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html Tom On Oct 18, 2013, at 10:09 AM, "Tartaglia,Lawrence J" wrote: > Hi Tom, > > Thank you for getting back to me. I should have been a bit more clear. What I want is the exact "central" section. I'm not sure if you are familiar with cryo-electron microscopy? I used a box size of 143 pixels to box my virus particles. What I would like to see if image 72 (central section) of my reconstruction. Is there a way to do that? I've attached an image of an example central section (left hand side) using the program IMOD. I'm sorry for the confusion... > > Best, > > Lawrence > > > On Thu, 17 Oct 2013 09:43:43 -0700, Tom Goddard wrote: >> Hi Lawrence, >> >> I'm not sure what you mean by "exact cross-section". Do you mean >> aligned to the virus map grid axes? If so the Orient button at the >> bottom of the volume viewer dialog will do that. But probably it is >> better to simply specify which planes to show using the Region Bounds >> panel of the volume viewer dialog (Features menu) - specify a z range >> 120 125 1 to show planes 120 to 125 using step 1 (i.e. every plane). >> This will be better than using clip planes. >> >> Tom >> >> >> On Oct 16, 2013, at 11:35 AM, "Tartaglia,Lawrence J" wrote: >> >>> Hello, >>> >>> I have a cryoEM map of a virus that I'm visualizing in chimera. I'd like to get a perfect cross-section of the map that I can use for publication. I've used the "side view" tool, but I can't get an exact cross-section. Are there any options to achieve this? >>> >>> Thanks! >>> >>> Best, >>> >>> Lawrence >>> -- >>> Lawrence J. Tartaglia, Ph.D. >>> Postdoctoral Scientist >>> Agbandje-McKenna Lab >>> Department of Biochemistry and Molecular Biology >>> College of Medicine, University of Florida >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> > > -- > Lawrence J. Tartaglia, Ph.D. > Postdoctoral Scientist > Agbandje-McKenna Lab > Department of Biochemistry and Molecular Biology > College of Medicine, University of Florida<Screenshot-1.png>

2 2

Cross-section question
by Tartaglia,Lawrence J 17 Oct '13

17 Oct '13

Hello, I have a cryoEM map of a virus that I'm visualizing in chimera. I'd like to get a perfect cross-section of the map that I can use for publication. I've used the "side view" tool, but I can't get an exact cross-section. Are there any options to achieve this? Thanks! Best, Lawrence -- Lawrence J. Tartaglia, Ph.D. Postdoctoral Scientist Agbandje-McKenna Lab Department of Biochemistry and Molecular Biology College of Medicine, University of Florida

3 2

Normal to the plane of the aromatic ring at the centroid
by Pande, Ajay K 16 Oct '13

16 Oct '13

How would I draw a normal to the plane of an aromatic ring, at its centroid? Thanks Ajay Pande

3 6

(no subject)
by edward el chamy 15 Oct '13

15 Oct '13

Hey i am a student using chimera 1.8 i have a question: how we find on a specific chain the different interaction domains? Thanks a lot

2 1

Fwd: setting or hardware problem?
by Chao Wang 14 Oct '13

14 Oct '13

Hi, chimera users I am starting to use ucsf chimera to analysis protein structure recently. It is an excellent software, and I have no problem using it at school. But when I try to use it on my other pc at home. It doesn't work properly. The ribbon looks flat and dull, not a 3D looking anymore, like the situation showed in pic1 and pic2. My hardwares: School PC: win7 64 bit,cpu E5-1606, Nvidia Quadro 5000, 4G Home PC: win7 64 bit, cpu i5-2500k, AMD Radeon HD6700, 8G I know the video card of school's pc is much better, but I checked the hardware list. HD6700 is also compatible. Can anyone tell me what is wrong? I really appreciate it. [image: Inline image 1] [image: Inline image 1] Jack Wang

2 1

Chimera commands to record MD movies
by psu4＠uic.edu 11 Oct '13

11 Oct '13

Dear Chimera, Since we run a lot of Amber MD simulation in remote clusters, we wonder if there is any Chimera command that can record the Amber MD trajectories remotely and save them as avi (or any other movie file formats)? If this is feasible, then we don't have to download all the trajectories to local and make the trajectory movies manually. We have searched the Chimera user manual but didn't see any command. If there are related commands which we didn't see, please forgive us : ) Thanks. * There is a way to activate X11 forwarding and use remote Chimera GUI to do this, but it's extremely slow and prone to freeze the computer. Cheers, Henry

3 4

font size in pull-down menus
by Boaz Shaanan 09 Oct '13

09 Oct '13

Hi, Is there a way to change the font size of the pull-down menus? For some reason on the Windows (XP) v.1.5.1 they seem smaller to me. Nothing in terms of graphics (or my eyesight) has changed since I upgraded to 1.5.1 recently. Thanks, Boaz Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

2 1

Packaging sessions
by Amedee des Georges 08 Oct '13

08 Oct '13

Dear Chimera, Currently, Session saves don't save volume data, only link to them, which is an issue whenever one of those links is broken or when one wants to send a whole session to someone else. Would it be possible to have an additional saving option that could be called "Package session" (like in InDesign), where a folder is created and all the files associated to the session saved in it. This way, people could zip and send the package by email, or package their important sessions to make sure not to lose them, or just to move them around. By advance, many thanks, Amedee -- Amedee des Georges Frank lab Howard Hughes Medical Institute Dept. of Biochemistry and Molecular Biophysics 650 W 168th St, P&S Black Building room 221 New York, NY 10032 (T) 212 305-9527 (F) 212 305-9500 (E) ad2720(a)columbia.edu http://franklab.cpmc.columbia.edu

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want to converge 20 pdb files of a trimer
by ashok rout 07 Oct '13

07 Oct '13

Hi, I have a nmr structure of a protein which is a trimer. I want to converge 20 pdb files of the trimer, by Chimera. And also want to converge a specific region of the 20 pdb files of the trimer. Can you please assist me how to do this?? Thanks, Ashok -- thanks & regards, Ashok

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Structural Allignment in Chimera
by Syeda Hira Batool 06 Oct '13

06 Oct '13

Hello I want to know how chimera does Structural allignment. I am writing a python script to allign protein structures(from MD simulations) and eventually calculate RMSD. Please can anyone provide me a source code or a helping material.Thanx in advance. Hira Batool Student of BS-Bioinformatics Biosciences Department COMSATS Institute of Information Technology Islamabad, PAKISTAN

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info pivotting on a single atom
by Christian Martinoli 04 Oct '13

04 Oct '13

dear all, I have troubles in setting the center of rotation on a single atom of my model. i'm working with the command line to build up a short clip at the end.what i would need is pivotting the whole model on the three axes, rather than in 2D as seems work with cofr command. any help? Thanks in advance Christian -- Christian Martinoli University Of Pavia Dept. of Biology and Biotechnology "Lazzaro Spallanzani" Structural Biology Lab. Via Ferrata 1, 27100 Pavia Italy

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command line to define a plane
by Jean Didier Pie Marechal 03 Oct '13

03 Oct '13

Dear all, is there a way to define a plane from the command line. Something that would work providing a list of atoms or a selection. Cheers, JD Dr. Jean-Didier Maréchal Associate Professor The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es

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Re: [Chimera-users] Question about multi align viewer
by Elaine Meng 03 Oct '13

03 Oct '13

On Sep 20, 2013, at 9:33 AM, Sean Connell wrote: > Hello I was wondering if it is possible to calculate conservation statistics using only subsets of the aligned sequence. The reason I ask is that in my alignment I have differently families of proteins that have slightly different functions and I would like to highlight residues that are conserved in one subset but not in the other? > Hi Sean, Not directly. I believe you would have to create alignments of just those subsets. You could do that with some other program (including text-editor) before opening the alignment in Chimera, or you could do it in Chimera. Of course, keep the original file with the full alignment too! To edit in Chimera, open the full alignment and then from the sequence window menu choose "Edit... Delete Sequences/Gaps" and in the resulting dialog, choose which sequences to delete. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> You can then continue working with the subset alignment in Chimera, including saving it to a new file (sequence window menu "File... Save As"). 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 P.S. your original message was in an attachment, which was kind of weird, but I could view it by just clicking the attachment

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Stereoscope viewing
by Thompson, Matthew K 02 Oct '13

02 Oct '13

Can anyone recommend the best camera settings for stereoscope glasses? Mine just don't seem to turn out right.

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electrostatic surface calculation
by Ursula Schulze-Gahmen 02 Oct '13

02 Oct '13

I calculated the coulombic surface and the electrostatic surface for my molecule. They show a significant difference in the shape of a small surface area. For the electrostatic surface, I converted the pdb file into a pqr file using the pdb2pqr called from chimera. Then I ran APBS also from within Chimera. When I display this surface it exhibits a strong protrusion in an area where there is no side chain. This protrusion is not present in the Coulombic surface. Any idea where this is coming from? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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how to write script that can run chemera command
by 张海平 30 Sep '13

30 Sep '13

Dear professor: I find a command "delete ligand" can delete ligand from a protein. Then I have thousands of protein contain ligands, how can I write a script to do this command automotically, Thanks for your kindly help. Best regard Haiping Zhang

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Editing Question
by Kirk Moldoff 30 Sep '13

30 Sep '13

Hi, I'm working with a pdb model 3ALQ. It is a Tumor Necrosis Factor and its TNFR receptor. I'd like to be able to turn off the bound TNF. Or select it for deletion. Can't figure how to do this. Any suggestions? Ultimately I'd like to be able to save just the TNFR as a .pdb file. Thanks, Kirk -------- Kirk Moldoff www.galeriekirk.com 609-252-9479

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Generating a PDB file
by Nathalia Varejão 27 Sep '13

27 Sep '13

To whom it may concern, I'm using the chimera to visualize a protein ligand docking, but I want to save the best model as a PDB file that I can use anywhere to perform other analysis, is it possible? For example, the pdb that I saved by the chimera do not open in PyMol viewer... Can you help me? Nathalia

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STL file questions
by David Gene Morgan 26 Sep '13

26 Sep '13

Hi, I have a couple of questions about the chimera STL files. I tried to open one using chimera to determine whether they contain any color information, but I wasn't able to open the file I just wrote. I don't care about that, but I would like to know if they contain color information. Is there any way to control the degree of tesselation when writing an STL file? In other words, some STL files are huge because they contain huge numbers of triangles (and some 3d printers can't handle overly large files). I am wondering whether it is possible to control the size of the output files, which is effectively asking if it is possible to control the number of triangles in the file, how finely sampled the model is, etc. (however one wants to describe that property). Finally, as I understand STL files, they are usually "unscaled" (i.e., the co-ordinate system describing the vertices of the triangles doesn't have fixed length units). Is that true for the STL files chimera creates? If I wanted to create two models with an accurate reflection of their relative atomic sizes, are there tricks I will need to employ? -- David Gene Morgan Electron Microscopy Center 320C Simon Hall IU Bloomington 812 856 1457 (office) 812 856 3221 (3200) http://bio.indiana.edu/~cryo

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Calculating SAS areas for selected residues for a whole trajectory of structures
by Harald Lanig 24 Sep '13

24 Sep '13

Dear Chimera users, I am currently using chimera to calculate the solvent accessible surface for several selected residues of a single structure (I am using the Attribute calculator with the formula sum(atom.areaSAS) to do this). Is there a way to apply this to a set of structures coming from a molecular dynamics trajectory? I am interested in how the solvent accessible surface of a set of residues changes during the simulation. Any hint is highly appreciated! Best wishes, -Harald -- ------------------------------------------------------------------------ PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen Phone +49(0)9131-85 26525 harald DOT lanig AT fau.de Fax +49(0)9131-85 26565 http://www.chemie.uni-erlangen.de/lanig ------------------------------------------------------------------------

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Building DNA along A PBD Using RNA command
by Joshua Carter 23 Sep '13

23 Sep '13

Hi, I'm working on a project in chimera that involves modeling the binding of a RNA-guided protein complex to a double stranded piece of DNA. What I need to do is be able to is either match a DNA pdb to the existing RNA pdb I have or build one using the rna command in chimera. I know there is a path command, is there any way I could specify that to build along a pdb I have already? Or am I just barking up the wrong tree entirely? Thanks,Josh

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Question about multi align viewer
by Sean Connell 20 Sep '13

20 Sep '13

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selecting a specific residue
by Elaine Meng 19 Sep '13

19 Sep '13

On Sep 18, 2013, at 8:53 PM, Serina Doolittle <serinadoolittle(a)me.com> wrote: > Hi again, > > So now i have another question... > I have selected the ligand because that is what my research mentor and I are interested in (the active site and ligand binding etc.) however, when i select "ligand" it also high lights other molecules around the protein, more around the surface, like butanol - how can i just select the ligand NADPH and not have to select the other small molecule ligands that are not part of the active site of the protein? can i do that? > > Serina Doolittle > Thanks! > Hi Serina, The "ligand" detection uses automatic rules and won't always get what you expect, but there are many other ways to select a specific residue. For example, you can select by residue name and/or number, or with the mouse in the Chimera window. With mouse: Ctrl-click on some atom selects it, and then keyboard up arrow will promote the selection to the whole residue. With command: specify residue name or number, e.g. select :nad select :254.a … would select residue named NAD, or residue 254 in chain A respectively. How do you find out the residue name or number? One way is by hovering the mouse over some atom or bond in the residue, which will pop up a balloon that shows atom name, residue name, and residue number. With menu: Select… Residue… allows selecting by name (all the residue names present will be listed in the menu). NADPH might have residue name NAP, NAD or something like that, since PDB files have 3-letter residue names. That would select all residues of that type, so you'd probably want to use one of the other methods if there are multiple NADPH molecules and you only wanted to select a particular one. Manual pages on selection and command-line atom specification: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> Also, you may want to look through the "getting started" tutorial to become more familiar with Chimera. <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> 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

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Hello
by A Amiri 19 Sep '13

19 Sep '13

Hello. I have a problem with chimera! i want to join two pdb file together by C-N peptide bond. Actually this is a modeling of a fusion protein that one part of its, is a protein and another part is a linker. I need a complete structure. I select the carbon atom from one model and nitrogen atom from another model. I use the "build structure<join modesl" menu for this purpose but the "apply" button is inactive still and i don't know how i can activate it! please help me. ________________________________

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Re: [Chimera-users] vop cover
by Elaine Meng 18 Sep '13

18 Sep '13

Hi Pradeep, That message is saying you must specify the density map. I.e. if the atomic structure is model #0 and the density map is model #1, the command could be something like vop cover #1 atom #0 Command usage and options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover> Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. it is recommended you send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of to me directly - thanks! On Sep 18, 2013, at 2:02 PM, Pradeep Pallan wrote: > Hi Elaine, > > I was looking at using vop cover. I have a case where part of the molecule > is not within electron density box. The map cuts off at the unit cell dimensions, > and my space group is P1. Where I need edensity is approximately at y= -10. > When I try the command > 'vop cover "atom"', it gives the message "file.pdb is not a volume". > > Is this the right way of getting the molecule covered in e density or do I need > to use a different option. > > Thank you, > PP

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Problem Using Transparency Command in Chimera
by Joshua Carter 18 Sep '13

18 Sep '13

Hi, My name is Josh Carter and I am an undergraduate researcher working at Montana State University. I am using chimera to make a movie a a protein complex interaction and I'm having trouble with the transparency command. When I type in just the command into chimera it doesn't even recognize it as a command. surftransp works but transp or transparency aren't recognized. Is there a bug fix I can run for this? Thanks,Josh

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How to determine the distance from SG of Cys to the centroid of a nearby Trp ring
by Pande, Ajay K 17 Sep '13

17 Sep '13

I am using Tools/Structure Analysis/Axes -Planes-Centroids. Selecting the Trp Indole ring, obtaining the centroid. Then selecting SG of Cys and the centroid and drawing an axis. That axis does not seem to pass (exactly) through the SG and Centroid- that' my first problem, the 2nd problem is to get the distance between the centroid and SG.

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colour by attributes is only colouring one chain of the dimer, how to make the colouring apply to both chains of homodimer
by Anne-Frances Miller 17 Sep '13

17 Sep '13

Dear team Chimers 1- Thank you for GREAT software ! 2- How to make the colouring apply to both chains of homodimer ? I have a homodimer in which features of the active site derive from both monomers so the degree of active site conservation will only show up if I can apply colour by attributes to both monomers (attribute will be conservation) Right now, colour by attributes is only colouring one chain of the dimer, chain A. Anne-Frances Anne-Frances Miller Professor of Chemistry Director, Magnetic Resonance Centre University of Kentucky Dept. Chemistry, 505 Rose Street Lexington KY 40506-0055

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Chimera Questions
by Serina Doolittle 16 Sep '13

16 Sep '13

Hi, My name is Serina Doolittle. I am an undergraduate research student at Armstrong Atlantic State University in Savannah, Ga. I am currently using Chimera to build two protein models. I have the proteins in the form that I want them in to 3D print. However, one of them is not a single chain protein. It has chain A and B. I hid chain B and focused on chain A because of the simplicity for the 3D protein model that I want. However, when you hide chain B and you put chain A on "show surface" that are like little holes or blotches missing from the protein where chain B is suppose to be. Is there anyway that I can fix this problem and single out chain A to make it look like it is completely lone in the "show surface" view. If you would like I will send you the Chimera file ("session"). That way you can visualize what I am trying to do. Serina Doolittle serinadoolittle(a)me.com 912-665-3259 Armstrong Atlantic State University Student

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How to move a domain in mouse mode /move selection
by Juergen Joachim Mueller 12 Sep '13

12 Sep '13

Hallo, how can I move a domain consisting of 3 chains using mouse mode/ move selection? I will use chain A: 6-121, chainB: 7-103, Chain C: 6-103. The selection by command line takes always the longest number 121 for all three chains - A:6-121, B:7-121, C:6-121. Greetings, Jürgen (Chimera production version 1.8 (build 38824) Windows8)

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How to modify a structure to put some atoms in a plane....
by Sergio Garay 12 Sep '13

12 Sep '13

Hi all I'm trying to put a Nitrogen atoms of a Nitro group in the same plane that a imidazol ring, but until now with no success. I've tried using modify structure and changing the bond and geometry of the carbon to which the Nitrogen is joined, but it did not work. I attached an image with the problem. I've also tried to minimize the structure using AMBER ff (despite I know that this ff is not appropriate for small organic molecules) but it can fix the problem. May be I'm not clear enough so, I summarize: I want to put the Nitro group in the same plane of a imidazol ring (look at the picture, please). Any advice will be appreciated. [image: Inline image 1] Sergio -- Sergio Garay Dr. en Ciencias Biológicas Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

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Solvent Channel Dimensions
by Thompson, Matthew K 12 Sep '13

12 Sep '13

How can I measure the dimensions of a solvent channel in a protein? The channel is clearly visible after the surface in generated. In addition, the cavity can be created with Surfnet. Something like "Measure and Color Blobs" does not give the dimensions I need. I am interested in the width of the channel at its most narrow point. Thanks Matt

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Re: [Chimera-users] automatically calculated labels for quantitative tomography data
by Tom Goddard 11 Sep '13

11 Sep '13

Hi Martin, Thanks for the detailed explanation. I think a generalization of your idea might be useful to more people. Basically you could create a text label including an automatically updated numeric value, but that number could be calculated from a density map contour level, or a molecular dynamics trajectory energy value, or a distance between a residue and ligand during a conformational change -- in other words the numerical value could measure many things. The case of just density map threshold levels has some utility, but since the same value can be seen in the volume dialog where you actually change the value, it seems more for presentation than analysis. The general tool would take significant work, because Chimera doesn't have a framework for providing measurement updates. We are working on the next generation of Chimera and this graphical label idea is interesting because we are looking at having fewer dialogs -- even a Chimera in a web browser. Maybe instead of using a separate volume dialog you could just display the threshold levels like you have done, and simply use the mouse to directly change those values in the graphics window. You've mentioned movie making. The labeling in your figure can be included in Chimera movies now, and the values can change, and labels fade in and out. Most Chimera movies are made with command scripts and these label operations would use the 2dlabels command. Granted with your proposed tool it might be easier to make the movie, but I'd say only slightly easier, because the overall movie making is not simple and the labels are just one small aspect. I have worked with Carolyn Larabell's group looking at their x-ray tomography data using Chimera some years back. They concluded Amira better suited their needs for doing segmentation. Here is a demo I gave showing what Chimera could do with their Pombe cell tomography. http://www.cgl.ucsf.edu/chimera/data/ncxt-feb2008/xraytomography.html Tom On Sep 11, 2013, at 5:05 PM, Martin de Jonge wrote: > Hi Tom, > > Thanks for the reply. I guess you raise a few questions, so I'll try and pick them individually. > > 1. the concept > >>> Or maybe it doesn't need a separate window -- you might just be able to say display colored labels in the graphics (e.g. "Zn 11" "Cu 47" "Ca 1500") for several density maps that list both an element name and the current contour level. You could control those levels using the Volume Viewer dialog and the labels would automatically update. > > Yes, I think that's what I was thinking. In the image I linked you to earlier, the threshold levels were manually entered into the color key. Every time the threshold changed these entries had to be updated also. In the new implementation one might enter into the color key dialog: "Ca {#3 * 1000}", where "#3" represents the threshold level for model number 3, the " * 1000" indicates multiplication by 1000, and the curly brackets indicate the presence of a substitutional expression. (Of course you would want to make this syntax consistent with Chimera!) > > The thinking about the simple mathematical operations is that sometimes the reconstructed data is only relatively scaled, and needs a final conversion factor to become a 'real' unit. Alternately, one might have data in ng/µm^3 and wish to convert to ug/cm^3, in which case multiplication by some power of 10 would be nice. In other cases the mathematical function could enable a change from units of mass/volume to molarity. Don't worry too much about this idea - it is probably not worth the effort, and can probably be performed by other means. > > 2. the user base > > I agree that at present there is not much call for this feature, however I note that two forms of x-ray tomography have recently entered the quantitative domain: x-ray fluorescence tomography (now performed by 10+ groups around the world) and soft-x-ray absorption tomography, performed most notably by the group of Larabell and LeGros at the UCSF (see eg http://www.ncbi.nlm.nih.gov/pubmed/21360734) (have you made contact with that group? I /think/ they render with Amira, but they are putting heaps of computing effort into automated segmentation of their LAC data, and I imagine this could be a good team to collaborate / share resources with). But I appreciate that the tomography user base would not rise to 1000 within 5 years, and therefore that this extension may not be practicable. > > I think this feature would be useful for the other main Chimera user base, which I gather is the protein crystallography (PX) / molecular modelling / imaging people. I guess my thinking here is that one of the great features of Chimera is the ability to explore the dataset dynamically, by adjusting thresholds, rotating, etc. This applies also for molecular / PX data. For all cases it is useful to adjust the threshold (being now generalised to either linear absorption coefficient (LAC), elemental concentration, or electron density) to see different features. This is usually done with the slider, or from the cmd line, but can also be scripted in movies etc. My suggestion (that I think you have understood in general, but repeat for clarity) is that there could be a mechanism to display the present threshold in a key on the display window. As such it could be one (electron density, LAC) or several (elemental concentration) numbers that are transferred into the key. > > Why am I saying this? Just in case you think there might be some other call for this feature from the other user base! I leave it to you to decide, and fully accept your knowledge of the Chimera user base! > > Thanks for the response, and for developing a great piece of software. Let me know if there is anything I can do in return (besides acknowledgement / citation!). > > [PS - I took the chimera-users off the response just in case you think the Larabell comments are politically sensitive. I don't mind if they go out - I stand by my words - I'll leave it to you to decide, and to forward the mail to the development team as you see fit.] > > Yours, > > Martin de Jonge > > > > > > -----Original Message----- > From: Tom Goddard [mailto:goddard@sonic.net] > Sent: Thursday, 12 September 2013 8:16 AM > To: Martin de Jonge > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] automatically calculated labels for quantitative tomography data > > Hi Martin, > > Your elemental abundance tomography is interesting. I'm not sure I understand your Chimera suggestion. Do you mean there would be a separate window that lists the threshold levels for Zn, Cu, Fe, Mn density maps in type-in fields and adjusting the values would both change the contour level (as is done by the Volume Viewer tool) and update the labels displayed in the graphics window (as with the 2D Label tool)? Or maybe it doesn't need a separate window -- you might just be able to say display colored labels in the graphics (e.g. "Zn 11" "Cu 47" "Ca 1500") for several density maps that list both an element name and the current contour level. You could control those levels using the Volume Viewer dialog and the labels would automatically update. (By the way, did you know you can display 6 or 10 histograms in the Volume Viewer dialog instead of the normal limit of 3? Use volume dialog menu Features / Data Display Options and change "Maximum number of Histograms.", and use Features / Save Default Dialog Settings if you want that to be the default for future Chimera uses.) I don't understand what you mean by "include simple mathematical operations". > > If I understand your basic idea, I think it is specialized enough that only a few Chimera users would use it. I'm not sure I've ever seen a figure like yours with values that correspond directly to density map levels, because usually the density map values have some meaningless normalization. Most often presentation figure keys need to be created in an entirely custom way appropriate to the content of the figure. Still I think the feature you suggest would be cool, but given the hundreds of improvements people have requested we try to work on ones that lots of Chimera users (500 or 1000) will benefit from, or requests that allow you to do something that isn't otherwise possible. > > Tom > > > On Sep 10, 2013, at 7:56 PM, Martin de Jonge wrote: > >> Hi all, >> >> this might sound like a strange feature, but I use Chimera to render quantitative tomography data. I typically render somewhere between 2 and 6 separate elements (i.e., Zn, Cu, Fe, Mn, etc) and present these with a colour key, along with a numerical value to indicate the threshold concentration (typically in mmol or similar unit). There is an example of such data in: http://www.pnas.org/content/107/36/15676/F1.expansion.html >> >> When exploring such data it is very useful to adjust the display threshold, as various anatomical features appear at very different concentration levels. My suggestion / request is to have a numerical field in the colour key that can be linked to (eg) the per-model thresholds to indicate the concentration threshold at that moment. This would be particularly useful for making movies for presentations and articles. >> >> Some thoughts on useful properties of this numerical field: >> >> - it should inherit the colour of the colour-key label that it is associated with (or be able to select to be inheritable) >> - it could include simple mathematical operations, for when there is a simple relationship between the data and the reportable concentration eg, *, /, +, - >> - one should be able to specify the format of the number (using the usual formatting codes). >> >> thanks >> >> Martin de Jonge >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > >

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automatically calculated labels for quantitative tomography data
by Martin de Jonge 11 Sep '13

11 Sep '13

Hi all, this might sound like a strange feature, but I use Chimera to render quantitative tomography data. I typically render somewhere between 2 and 6 separate elements (i.e., Zn, Cu, Fe, Mn, etc) and present these with a colour key, along with a numerical value to indicate the threshold concentration (typically in mmol or similar unit). There is an example of such data in: http://www.pnas.org/content/107/36/15676/F1.expansion.html When exploring such data it is very useful to adjust the display threshold, as various anatomical features appear at very different concentration levels. My suggestion / request is to have a numerical field in the colour key that can be linked to (eg) the per-model thresholds to indicate the concentration threshold at that moment. This would be particularly useful for making movies for presentations and articles. Some thoughts on useful properties of this numerical field: - it should inherit the colour of the colour-key label that it is associated with (or be able to select to be inheritable) - it could include simple mathematical operations, for when there is a simple relationship between the data and the reportable concentration eg, *, /, +, - - one should be able to specify the format of the number (using the usual formatting codes). thanks Martin de Jonge

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Re: [Chimera-users] accuracy of fitting atomic structure in density map at different resolution
by Tom Goddard 11 Sep '13

11 Sep '13

Hi Andy, Do you mean how much fits vary depending on EM map resolution? I suppose you could apply Gaussian filtering to the EM map to produce a lower resolution EM map, then fit your atomic model, then see how much motion and rotation there is of a fit at one resolution from a fit at another resolution. All that is easy in Chimera. To compare different fits I would open multiple copies of the same atomic model and fit one to each different map then use the "measure rotation" command (e.g. "measure rotation #2 #3") to see how much motion there is between fits. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation With any other fitting software you could do the same test by exporting the Gaussian smoothed maps from Chimera, fitting with other software, writing out fit PDBs with the other software and then loading those PDBs in Chimera and comparing their orientation. In that case you'd want to use the Chimera "match" command to measure the motion between models (e.g. match #2 #3 showMatrix true, the look in Reply Log for results). The "measure rotation" only reports coordinate frame motions done within Chimera, whereas "match" aligns two atomic models. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html Tom On Sep 11, 2013, at 7:13 AM, Anindito Sen <emailanindito(a)yahoo.co.in> wrote: > Hi Tom, > > Is there any method by which, we can figure out the accuracy of docking of an atomic structure into its EM density map generated at different resolutions and by different software packages? > > Thanks > > Andy > >> Dr. Anindito Sen (Ph.D) >> Department of Cell Biology & Anatomy >> Graduate School of Medicine >> University of Tokyo >> Tel & fax: +81-3-5841-3339 >

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Minimization units
by Elisabeth Ortega 09 Sep '13

09 Sep '13

Dear Chimera dev. team, I have a very simple question regarding Energy Minimization. The energy units are kcal/mol or kJ/mol? In this function, chimera uses the MMTK function to calculate the energy, and, as far as I know, MMTK energy units are kJ/mol (in share/MMMD/MMTKinter.py the units of the length are corrected to angstroms, but the energies don't). I took a look in the previous e-mails of the chimera-users list. I saw some texts that refers to the energy in kcal/mol and I am a bit confused. Thank you for your time. -- Elisabeth Ortega Carrasco, Ph.D. Student Molecular Modelling of Transition Metal Systems Group Lab. C7/153, Chemistry Department Universitat Autonoma de Barcelona Tel.: +34935812857 email.: eortega(a)qf.uab.cat

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Querie: Ligand superimposition
by Graziella Portelli 09 Sep '13

09 Sep '13

Dear Chimera Team Hope this email finds you in good health. I am using UCSF Chimeria for my de Novo drug design disseration. I am still learning the basic functions that this software offers, however have not been able to figure out the following. Basically I need to put into one picture/frame the original ligand or my receptor and the possible ligands (generated by Ligbuilder). They have the same general structure with some changes and I need to superimpose them, but show them at separate levels. Is this possible to do this for only the ligands and not the receptor protein? I eagerly await your reply, Graziella Portelli B.Pharm

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Color Isosurface in Chimera
by Gregor Weiss 05 Sep '13

05 Sep '13

Hello, I tried to color different parts of an isosurface obtained by an electron cryotomogram to point out structures more clearly. Unfortunately, I didn't figure out how I can select different areas and color them differently. Which tool fits here the best? I can determine an area and subsequent color all structures in this area with the tool "Color Zone", but I was not able to select another area and choose a different color. Thank you very much for your help! With best regards, Gregor Weiss -- Gregor Weiss, B.Sc. Summer Researchassistant Jensenlab California Institute of Technology, HHMI Mail code 114-96 1200 E. California Blvd. Pasadena, CA 91125 626-395-8848 (phone)

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about the command: match
by 韩晓东 05 Sep '13

05 Sep '13

Dear sir, it is no doubt the UCSF chimera is a very excellent software. However, when i use the command: match iterate 2.0 site2 site1, a problem appeared as follows: unequal numbers of atoms chosen for evaluation. would you kindly share me the skill to deal with this problem. thank you very much for your time. sincerely yours, xiaodong han.

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Re: [Chimera-users] Chimera hbond
by Elaine Meng 05 Sep '13

05 Sep '13

On Sep 5, 2013, at 2:40 AM, Neha Gandhi <n.gandhiau(a)gmail.com> wrote: > Hi Elaine, > > I was going through your response on chimera mailing list regarding > saving h-bond analyses during MD ensemble/movie. Either one can write > files every nth frame or save log files. Is there a way to put all the > output of the frames one by one in one single file? > > Your help is appreciated. > > -- > Regards, > Dr. Neha S. Gandhi, > Curtin Research Fellow, > School of Biomedical Sciences, > Curtin University, > Perth GPO U1987 > Australia > LinkedIn > Research Gate Hi Neha, Writing the information to the Reply Log does not save a file. You can accumulate multiple sets of results in the Reply Log and then, at the end, save the Reply Log contents to a single file. The "findhbond" command has two separate options to write results to a file ("saveFile true") and to write results to the reply log ("log true"). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html> You can save the contents of the Reply Log (in menu under Favorites) to a file with its Save button. 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 P.S. please send chimera questions to chimera-users(a)cgl.ucsf.edu (CC'd on this message) instead of to me directly - thanks!

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display atom by coordinates
by Bala subramanian 03 Sep '13

03 Sep '13

Friends, I am trying to visualize the md movie of a channel protein. In every frame, i want to display only those ions whose Z coord ranges from -10 to 35 (zcoor of the channel) to make the movie. Is there any simple way ?. Precisely displaying atoms with a condition. Thanks in advance, Bala -- C. Balasubramanian

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Linking two chains in a PDB file
by Maxwell Cherf 03 Sep '13

03 Sep '13

Hi Sir/Madam I have a PDB file of three proteins bound together (in one model). I would like to fuse the N terminus of one protein to the C terminus of another protein by adding a peptide linker between the termini. Is it possible to do this using Chimera? So far, I have built a linker and joined it to one of the termini, but doing that combined the linker and all proteins in the file into one model. Now, I can't connect the free end of the linker to the other terminus because they are part of the same model. Any help would be much appreciated! Best, Gerald Cherf, PhD candidate Cochran Lab Bioengineering Department Stanford University

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problem with SwissSidechain plugin installation
by Thomas Evangelidis 03 Sep '13

03 Sep '13

Greetings, I have a problem with SwissSidechain Chimera plugin in Linux 86_64 (Centos 6.3). I followed the instructions yesterday and could use it to create a D-peptide: http://swisssidechain.ch/visualization/chimera.html However today I can't. I tried to add it several times to Preferences->Tools->Locations without any luck. I even did a fresh install of the current stable release and rebooted but I still can't use it. I remember I encountered similar problems in the past. Do you know what's wrong? Thomas -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tevang(a)pharm.uoa.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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help
by rajan sreekanth 30 Aug '13

30 Aug '13

Hi, I had morphed two conformations (open and close) of my protein using 'Morph Conformations' tool. I want know whether we can save the coordinates capturing the intermediate states? Something like an NMR ensemble consisting of the open-intermediate states-close conformations as a single PDB file? Thanks Sreekanth

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Re: [Chimera-users] building a peptide
by Elaine Meng 30 Aug '13

30 Aug '13

Hi Kumud, You would just specify the phi and psi angles for "turn" when building the peptide. You can specify a different phi and psi for each residue if you want, in the peptide building dialog. You do not have to use the values supplied for alpha and beta, you can enter any values, as described in the instructions: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> Also, in a peptide structure that already exists, you can change phi and psi for each residue, either ...by rotating the bond interactively (see the Adjust Torsions tab in Build Structure): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> or ...by changing the "phi" and "psi" attribute values in the Selection Inspector (select an amino acid residue in a peptide or protein, click green magnifying glass near bottom right of Chimera window to open the Inspector, Inspect: "Residue" and change the values for "phi angle" and "psi angle") <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html> However, it is up to you to specify reasonable values. You can check the Ramachandran map by using the "Ramachandran plot" function in the Model Panel (under Favorites in the menu). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/rama…> Although it is possible to build a whole protein with different secondary structures, it would probably have many severe problems (packing etc.) and the basic peptide-building in Chimera is *not* intended for this purpose. You might want to look into using some other program to predict structure instead, or modify an existing protein structure instead of building the whole thing from scratch. There are probably hundreds of programs and dozens of web servers to predict protein structure, but it is beyond the scope of the chimera-users list and my knowledge to discuss the possibilities. 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 Aug 29, 2013, at 11:50 PM, Kumud Agarwal wrote: > Hi, > Thank you for your help. > Is there any way to build a beta sheet in Chimera? How can I introduce > turns in between the strands in beta sheet using the build structure > option in chimera?

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Chimera VTK file reader
by Tom Goddard 29 Aug '13

29 Aug '13

Hi Andrew, I added a VTK file reader -- in tonight's Chimera daily build. It handles vtk structured points files in ascii format like the one you gave me. Your file had many -32768 values which seem to indicate regions where you don't have data and normal data values in a range 0 to 55. This makes the histogram display of data values in Chimera worthless because the data range is 33000 but the meaningful range is 55. Chimera is only able to show the whole range. You might want to use some other value to indicate "no data", like -1 if negative values are not valid. Tom > On Aug 6, 2013, at 10:09 AM, Andrew VanBenschoten wrote: > >> Hi Elaine, >> I hope all is well! Quick question for you: I have a 3D .vtk file (attached) that I want to be able to view in Chimera. This is one of the diffuse scatter maps that we discussed earlier: nearly identical to X-ray diffraction patterns except that the data values are applied to entire voxels as opposed to points. Any suggestions as to what I could try? Thank you so much! >> >> -Andrew >> <out.vtk> > >

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building a peptide
by Kumud Agarwal 28 Aug '13

28 Aug '13

Hi I am very new to Chimera. I am using Chimera version 1.8. I am trying to build a peptide in chimera in beta strand conformation using build structure option but the generated peptide did not show beta strand. Why is it so? Thanks, Kumud Agarwal IIT Bombay India

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Make bonds in a large polypeptide
by Francesco Pietra 27 Aug '13

27 Aug '13

Hello; Is there a limit in the number of atoms when using the function "make a bond"? I was trying that in a polypeptide of 450 standard residues (I made it a single model) and it did not work. Just to not be cryptic, that need arises from having modeled by special techniques the initial portion of the polypeptide. Now I would like to replace that portion with the modeled one. I had restrained with rmsd-colvars the dihedrals of a short stretch of alpha helix, so that I could align the modeled portion with the polypeptide. thanks francesco pietra

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some questions about new features, in particular MD
by Lionel Nauton 24 Aug '13

24 Aug '13

Hello I was very pleasantly surprised to discover a molecular dynamics module in the latest version of chimera, I used already "MD movie" to see the dynamics with NAMD made, but the ability to make dynamic from chimera is a real plus, thank you for that. in spite of this, one thing I do not understand why the minimization phase is parallelizedin the dynamics module and is not in standard mode, is a planned evolution, I'm too impatient? Second, in the latest version (21-08-2013), I can not read trajectories files from GROMACS , I saturate the RAM (16 GB and 7 GB swap) and the program exits.the same dynamics made with NAMD in .dcd formatworks well, any idea ? that's all thanks for your very good job.

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