September 2010 - Chimera-users - RBVI Mailing Lists

movie command with headless Chimera
by Tom Goddard 24 Sep '10

24 Sep '10

Hi Masako, You want to create a movie by running Chimera in the background (no windows, no console). You are trying the right approach, using "headless" Chimera. I'm afraid the movie command may not work with headless (ie background, no windows) Chimera. Headless Chimera can't create any dialog windows and it may be that the movie command internally relies on the Movie Recorder dialog. I don't know for sure. Your error is caused by the movie command trying to monitor changes in the Chimera graphics window (which does not exist). I can fix that and see if there are subsequent errors. I'll try this today or tomorrow. Image saving works with headless Chimera, but I have not tried background movie recording in the past -- obviously useful though. Tom > Hi, Tom. I hope you had a nice vacation :) > > I was able to run very simple command script with headless chimera, but I > am getting these errors trying to save a simple spinning movie... > > reading final.mrc 2.2 Mb 0% > Done reading final.mrc > final.mrc opened > reading final.mrc 18 Mb 0% > Done reading final.mrc > Traceback (most recent call last): > File "/home/mterada/opt/UCSF/Chimera-headless/share/chimeraInit.py", > line 422, in init > chimera.openModels.open(a, prefixableType=1) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/chimera/__init__.py", > line 1510, in open > models = func(filename, *args, **kw) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/Midas/ChimeraExtension.py", > line 32, in func > processCommandFile(cmdFile) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/Midas/midas_text.py", > line 104, in processCommandFile > _processFile(f, emulateRead, filename) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/Midas/midas_text.py", > line 135, in _processFile > if makeCommand(line): > File > "/home/mterada/opt/UCSF/Chimera-headless/share/Midas/midas_text.py", > line 65, in makeCommand > f(c, args) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/MovieRecorder/ChimeraExtension.py", > line 25, in doMovieCmd > doExtensionFunc(MovieRecorder.processMovieCmd, args) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/Midas/midas_text.py", > line 426, in doExtensionFunc > extFunc(*tuple(processedArgs), **kw) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/MovieRecorder/__init__.py", > line 207, in processMovieCmd > director = getDirector() > File > "/home/mterada/opt/UCSF/Chimera-headless/share/MovieRecorder/__init__.py", > line 342, in getDirector > director = Director.Director() > File > "/home/mterada/opt/UCSF/Chimera-headless/share/MovieRecorder/Director.py", > line 69, in __init__ > top = chimera.tkgui.app.winfo_toplevel() > AttributeError: 'module' object has no attribute 'tkgui' > Error while processing makeimage.cmd: > AttributeError: 'module' object has no attribute 'tkgui' > > File > "/home/mterada/opt/UCSF/Chimera-headless/share/MovieRecorder/Director.py", > line 69, in __init__ > top = chimera.tkgui.app.winfo_toplevel() > > See reply log for Python traceback. > > > This same command script saves spinning movie with no problem, so I am > guessing it's headless chimera not having GUI... Is there a way around > it? > > Thanks, > > Masako >

1 1

Mutagenesis
by r charbel maroun 23 Sep '10

23 Sep '10

Dear Chimera users, Please correct me if I'm wrong, but neither in Chimera nor in the user's list did I find any info on mutating a residue. Is this a missing functionality ? Greetings -- R. Charbel MAROUN, PhD, HDR Neurobiologie et Pharmacologie Moléculaire Centre de Psychiatrie et de Neurosciences Broca-Sainte Anne (INSERM U894) 2ter rue d'Alésia 75014 Paris FRANCE Tél. +33 1 40 78 92 77 Fax +33 1 45 80 72 93 e-mail rmaroun(a)gmail.com charbel.maroun(a)inserm.fr

2 2

Saving new coordinates after superimposing structures
by Sujata 23 Sep '10

23 Sep '10

Hi, After I superimpose two structures using MatchMaker, I would like to save the coordinates of #1 after being superimposed with #0. When I save the PDB with the new coordinates and open #0 and #1 PDBs again, they do not superimpose. Can this be done? What is the best way to achieve this? (Elaine, I have a third fragment I want to bond to the previously bonded one and since the first-second has moved now, I want to do this so that they are on the same axis). Thanks, Sujata

2 1

technical questions about volume viewer in chimera
by Alex Shkumatov 22 Sep '10

22 Sep '10

Hallo Perhaps, this has been on the forum before, but I could not find the answers to my questions: 1. Some EM density maps have a header. I wonder how Chimera recognizes it and calculates map dimensions? 2. Does chimera take default voxel size from header of EM file? Thanks in advance Alex ---------------------------------------------------------------------- Alexander Shkumatov, predoc -- Biological Small Angle Scattering Group EMBL Hamburg Outstation c/o DESY -- Building 25A Notkestraße 85 -- 22603 Hamburg -- Germany tel: +49 40 89902 178 fax: +49 40 89902 149 Email: shkumatau(a)embl-hamburg.de ----------------------------------------------------------------------

3 4

Re: [Chimera-users] Joining fragments in a peptide bond
by Elaine Meng 21 Sep '10

21 Sep '10

Hi Sujata, I'll answer the easy part first: you can specify the axis cylinder radius as an Angstrom value in the Define Axis dialog (opened from the Axes/Planes/Centroids tool) or if you are using the "define" command, with the "radius" keyword, see the general options in that page: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru…> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> I see you have a left-handed polyproline helix which also has a superhelical twist, and you wish to extend its length maintaining the same helicity and superhelicity. Then you have assembled three of these into a triple helix. This problem is not really something you want to attack with Build Structure; instead, you need to figure out the symmetry operations to extend this structure, then apply them to additional copies of the identical structure to extend it. One way would be to figure out BIOMT matrices and add those to the PDB file. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html#biomt> However, it can be difficult to figure out the correct values and edit them in using the correct format, so I'll describe a different way that just uses commands. The two fragments you sent are identical (I know you know this, I'm just explaining to the others), and I matched the first half of one copy to the second half of the other copy to try to figure out the symmetry operations. Command: match #1:1-15@ca #0:16-30@ca <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> This match looked pretty good to me, so next I used the measure command to tell me the transformation that had been used to generate this match: measure rotation #0 #1 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> Actually that command will display another axis cylinder, and I don't think you can control the size of that one, but you can just close or hide it with the Model Panel (under Favorites in the menu). The transformation information is given in the Reply Log (also under Favorites in the menu): Position of #1 relative to #0 coordinates: Matrix rotation and translation -0.00777505 -0.89851915 -0.43886545 45.94850252 0.89297961 -0.20375330 0.40133777 -0.02182236 -0.45002996 -0.38877748 0.80394347 -26.28870812 Axis -0.40352597 0.00570191 0.91495042 Axis point 17.07887792 12.85324577 0.00000000 Rotation angle (degrees) 101.75881858 Shift along axis -42.59440324 Then I reset so that the two fragments were again exactly superimposed (since they are identical ), using the command: reset <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html> Then I applied TWICE the reported translation and rotation because the match was of 15 residues, but the whole fragment is 30 and I want to join the ends. I used the axis given in the Reply Log as the axis of movement and the axis point as the center of rotation, and applied twice the rotation angle with the "turn" command and twice the shift with the "move" command: turn -0.40352597,0.00570191,0.91495042 203.5 models #1 coord 0 center 17.07887792,12.85324577,0 move -0.40352597,0.00570191,0.91495042 85.188 models #1 coord 0 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> At this point it looks like they are in a pretty good position to just add the bond and delete the extra atoms at the ends. Since you already have the models in position, don't use Join Models in Build Structure. Instead use "copy/combine" in the Model Panel (or the "combine" command) to merge the two fragments to create another model, and in that model, select the extra atoms that you want to delete (probably all hydrogens on N-term N and one of the oxygens on the C-term carboxyl of the other fragment), use command "del sel" to delete them, then select the two atoms to be bonded, and use command "bond sel". The bond will look a little strained, but this whole approach is going to get you an APPROXIMATE model. You could use command "addh" if you cared about the presence of the amide hydrogen at the join. This approximate model is good enough for a figure, or as a starting point for a simulation in some other package like Amber. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html> Actually, it might have been better to start with the trimeric fragment with all 3 chains, use residues from all 3 chains for the match, etc., and then there would be three bonds to form, rather than repeating only the single strand and then trimerizing. Hard to know without trying. Sorry, it is a rather laborious process. 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 Sep 20, 2010, at 10:31 AM, Sujata wrote: > Hello Elaine, > Thank you for the email below. It was very helpful. > > But, I would like the second fragment to be on the same helical axis as the first one. When I join them this way, by defining the torsion angle, the second one does not stay on the same axis as the first one. So is there a way that I can fix the two peptides to be on the same axis when I fix the bond length and the torsion? > > I am attaching the two individual files and the combined one. > > Also when one defines axis, is there a way to reduce the thickness of the displayed axis. Due to its thickness, the atoms are not visible. > Thank you. > > Regards, > Sujata >

2 1

question
by Domenico Raimondo 17 Sep '10

17 Sep '10

Hi, I have found on the MODELLER web page that Chimera has a Modeller interface in the latest nightly builds. Is it right? and is it possible to use it? Thanks a lot, Domenico. .............................................................................................................. Domenico Raimondo Researcher - Biocomputing group, University of Rome 'La Sapienza' Dep. of Biochemical Sciences, P.le Aldo Moro, 5 - 00185 Rome, Italy. e-mail: domenico.raimondo(a)uniroma1.it domenico.raimondo(a)gmail.com Web page: http://biocomputing.it/index.php/People/raimondo Skype name: domerai3 Tel (work): +39 06 49914297 Tel (mobile): +39 335 6475092 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.

3 4

defining attribute
by Bala subramanian 17 Sep '10

17 Sep '10

Friends, I want to define solvent accessibility as the attribute to create a worm representation. I used the template file 'percentExposed.txt' in the following link to create an attribute file. The sample file i creased is attached (exp.txt) http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/perce… when i give the command: deffattr exp.txt I get the following error. How to resolve the problem. Traceback (most recent call last): File "/usr/local/chimera_15/lib/python2.6/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/usr/local/chimera_15/share/Midas/midas_ui.py", line 260, in processCommand midas_text.makeCommand(text) File "/usr/local/chimera_15/share/Midas/midas_text.py", line 66, in makeCommand f(c, args) File "/usr/local/chimera_15/share/AddAttr/ChimeraExtension.py", line 33, in cmdAddAttr specInfo=[("spec", "models", "molecules")]) File "/usr/local/chimera_15/share/Midas/midas_text.py", line 424, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 77, in addAttributes return _addAttr(attrFile, models, log, raiseTool) File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 239, in _addAttr from ShowAttr import ShowAttrDialog, screenedAttrs ImportError: cannot import name screenedAttrs ImportError: cannot import name screenedAttrs File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 239, in _addAttr from ShowAttr import ShowAttrDialog, screenedAttrs

3 4

Display solvent-accessible surface?
by Hurt, Darrell (NIH/NIAID) [E] 17 Sep '10

17 Sep '10

Hi there, I’ve tried searching the archives and found some interesting information, but nothing specific to this question. Elaine’s response was particularly helpful: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003597.html >From the documentation, it seems that Chimera only displays solvent-excluded surfaces: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/representation.html… I understand that I can map solvent-accessibility to this surface using “Render Attributes”, but I would like to display the actual solvent-accessible surface. I want to do this because it is my understanding that electrostatic potential mapping to a solvent-accessible surface is often more informative than to a solvent-excluded surface: http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrosta… Can it be done? Thanks, Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62G Bethesda, MD 20892 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: 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.

2 2

Problem with Rainbow and "abnormal" PDB data
by Christian Schudoma 17 Sep '10

17 Sep '10

Dear Chimera-devs and community, I am "abusing" the 3D-rendering capabilities of Chimera to visualise 3D coordinates that do not actually represent molecular data. (Why do I do that? Because I love using Chimera for visualising molecular data and I needed a quick way to display (+ rotate/zoom) 3D data without hassle. I'm sure there are other solutions out there but I found it easier to convert my data to PDB than find a decent tool or code one myself.) I convert my xyz coordinates into PDB-format, using Hydrogen atoms and GLY as residue name (or, alternatively XXX - which wouldn't work either). I use the residue index (resSeq) to identify groups of points that belong together. This of course results in a complete nonsense-"protein" (with GLY-residues consisting of nothing but 100's of hydrogen atoms), which is nevertheless in syntactically correct (I hope) PDB format and both readable as well as displayable by Chimera (as a point cloud using wire-representation). Now to the problem I encountered: I would like to colour my "atoms" by their residue index. I can colour the individual "atoms" manually, using Select-operations or Ctrl-click and then the Color-menu. The Rainbow tool, however, does not work to colour my point cloud. It simply doesn't do anything. My question is, whether Rainbow performs some plausibility checking of the data (and if so, then whether it is necessary to do that? It would seem that Rainbow only needs to access either the residue, chain, or model indices to do what it's supposed to do, i.e. to assign colour)? Of course I am aware that my problem is kinda homemade and Rainbow works fine for normal PDB structures. I am also not saying that Chimera's buggy (although it seems to have a problem processing weird data in some situations (Rainbow) but not in others (manual colouring)). However, I'd like to understand why things don't work as expected ;) Cheers, Christian --- Christian Schudoma, M.Sc. Ph.D. Student Bioinformatics Group Max Planck Institute of Molecular Plant Physiology Am Muehlenberg 1 14476 Potsdam-Golm Germany phone: +49 (331) 567-8624 email: schudoma(a)mpimp-golm.mpg.de http://rloom.mpimp-golm.mpg.de

3 3

find the region around a volume imported from 3V voxelator
by Fabian Glaser 16 Sep '10

16 Sep '10

Daer chimera team, I am interested in finding a channel in a toluene hydrogenase, and extracting all the residues / atoms surrounding this channel. To do that I calculated the channel itself using the 3V voxelator (http://3vee.molmovdb.org), which produces a volume object that can be imported to chimera. See for example the output page http://3vee.molmovdb.org/viewResults.php?jobid=10sep02.ee6, which provides the file channel-004.mrc.gz, which needs to be first unzipped. When uploaded to chimera the volume is very clear and nice. But I want to find the residues/ atoms that form the channel, one the pdb itself 3DHG.pdb.gz, although the select and zone features seem to not work with the volume object. Any idea how to do that? Thanks a lot, Fabian -- ------------------------------------------------------ Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL E-mail: fglaser(a)technion.ac.il Tel: +972-4-8293701 Fax: +972-4-8225153

3 3

Chimera-users September 2010