- Chimera-users - RBVI Mailing Lists

Copy a pdb display configuration to another pdb model
by Tom Goddard 10 Mar '09

10 Mar '09

Hi Xiangan, I've added a new Chimera command "mcopy" to copy colors, display styles, coordinates and other settings from one molecule to another. mcopy #0 #1 will copy the colors, display styles (ribbon, stick, sphere, ...), and visibility (which atoms/residues shown) from molecule #0 to molecule #1. To copy other attributes such as atom coordinates, molecule placement (transform), or labels use the "settings" option: mcopy #0 #1 settings lxp copies just atom/residue labels, atomic coordinates and placement. The recognized settings are: c = color, s = style, v = visibilty, l = labels, x = coords, p = placement, a = all. The default is "csv". This command will be in tonight's Chimera builds. http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Tom Xiangan Liu wrote: > Tom, > I asked you a question in BPS meeting regarding the implementation of > copying a display configuration of a pdb file to anoth pdb with the > same sequences. Did you get chance to implement it into chimera daily > release? If yes, what is the command. If not, can you send me the > corresponding python codes to me? > Thanks, > > Xiangan >

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Atom Replacement
by Warren Menezes 10 Mar '09

10 Mar '09

** High Priority ** Hi! I was wondering if it is possible to replace a Selenium atom in a protein with a Sulfur atom? The reason is because Sulfur has parameters. Thanks! Warren M Chicago

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Re: [Chimera-users] converting a pdb to surface, then to obj
by Tom Goddard 10 Mar '09

10 Mar '09

Hi Dave, Yes, exporting surfaces from Chimera in Wavefront OBJ format does not include colors for multi-color surfaces. You have to export VRML, X3D, Povray, or Renderman formats for that. I know some people export to VRML then convert to OBJ with other software for import into Maya, but I have not seen any case where they carried the Chimera colors into Maya. If you figure out how to do that I'd like to hear about it. Tom Dav Tom wrote: > Daer Thomas Goddard, > > I recently saw your reply to export feature to obj. > > Is it true that there is no current support to export vertex color > (e.g. electronic potential surface color) through obj export format. > Only the vrml and x3d export include vertex color. > > thank you > > Dave. > > "Hi, I am trying to use pdb files to generate surface models (using > multiscale models) to convert to .obj files for use with Maya software. > I keep getting the same error and can't decide if I'm just not using the > command appropriately or if the is something else wrong with the files. > Any ideas?" >

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Re: [Chimera-users] Renaming chain directly in Chimera
by Elaine Meng 10 Mar '09

10 Mar '09

Hi Damien, For a more reliable response, please send mail to chimera-users(a)cgl.ucsf.edu rather than to me directly -- sometimes the others know the answer when I don't, and sometimes I'm away from work. Chimera doesn't provide a way to just choose some set of residues and give them any chain ID you want. It can reassign chain IDs if you are merging models, for example if you had two models that were both chain A, it could combine them into another model with chains A and B. However, I can't think of how that process could be used to do what you want in this situation. I've come across a few PDB-editing web servers, but I don't know which of these might do what you want. You may need to use SPDBV for pre- processing in this case. Here are the web servers in case they are of general interest: <http://www.igs.cnrs-mrs.fr/Caspr2/magicPDB.cgi> <http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/inputpage.html> Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Feb 27, 2009, at 9:40 AM, Damien Larivière wrote: > Dear Elaine, > > If a PDB structure contains 2 chains A and B, is it possible to > rename chain B as for example chain A directly in Chimera in order > to get one only chain ? Also, is it possible to rename part of > residues of a chain A (residues 256 to 312 for example) as chain B ? > > I ask this question because I often export low resolution surfaces > (obtained with Multiscale Models tool) in the vrml format or obj > format. However, I often have to color all the model (chains A and > B) in only one color and highlight a set of residues in another color. > > I know that I can do this by selecting the residues of interest, > coloring them by using Color zone, but the result is not exportable > in VRML (problem of vertex color or something like that). To avoid > export problem, it is very simple to rather rename chains and/or > reassign a letter to part of chain, which I do by using > SwissPDBviewer. So, can I do this in Chimera ? > > Thanks for your help > > Damien >

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WriteDMS with cofactors?
by Walter Novak 09 Mar '09

09 Mar '09

Hi All, I seem to have trouble with the dock prep procedure for molecules with cofactors, specifically NADP+. I cannot figure out how to write out the surface of both the protein and cofactor together. I can do this with the standalone DMS program using the "-a" flag. Am I missing something? I am using pdb 1el3 as a test and trying to redock the inhibitor I84 back into the complex. I completed the tutorial using 1abe and this was very valuable in learning how to prep molecules with DOCK. Thanks, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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program loading problem
by John Means 09 Mar '09

09 Mar '09

I previously had the latest release version of Chimera running on RedHat. Last week I ran the RedHat updater, and now Chimera will not load. When I run the program executable, the splash screen comes up, saying "Loading Tix" then the splash screen goes away. I've tried removing the Chimera directory and reinstalling the program, to no avail. Any suggestions or assistance would be greatly appreciated. -John Means

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Displaying a dimer from a monomer
by Eric Pettersen 09 Mar '09

09 Mar '09

(extracted from a bug report...) Dear Folks, How do I display a dimer, such as for 6RHN? So far I have been able to call up the monomer only, whereas the structure (and other evidence) shows it to be a dimer. Thanks, Sincerely, John Lowenstein

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converting a pdb to surface, then to obj
by Cheri Hampton 09 Mar '09

09 Mar '09

Hi, I am trying to use pdb files to generate surface models (using multiscale models) to convert to .obj files for use with Maya software. I keep getting the same error and can't decide if I'm just not using the command appropriately or if the is something else wrong with the files. Any ideas? Thanks, Cheri > <type 'exceptions.AttributeError'> Exception in Tk callback > Function: <function command at 0x1a44ab90> (type: <type 'function'>) > Args: () > Traceback (innermost last): > File > "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line > 1747, in __call__ > None > File "CHIMERA/share/chimera/baseDialog.py", line 244, in command > None > File "CHIMERA/share/OpenSave/__init__.py", line 210, in Save > None > File "CHIMERA/share/chimera/baseDialog.py", line 453, in OK > None > File "CHIMERA/share/OpenSave/__init__.py", line 161, in Apply > None > File "/home_local/cheri_local/chimera/share/ExportOBJ/__init__.py", > line 177, in write_surfaces_cb > write_surfaces_as_wavefront_obj(paths[0]) > File "/home_local/cheri_local/chimera/share/ExportOBJ/__init__.py", > line 184, in write_surfaces_as_wavefront_obj > mlist = surface_models() > File "/home_local/cheri_local/chimera/share/ExportOBJ/__init__.py", > line 147, in surface_models > mlist = chimera.openModels.list(modelTypes = [_surface.Surface_Model, > <type 'exceptions.AttributeError'>: 'module' object has no attribute > 'Surface_Model' -- `~: `~: `~: `~: `~: `~: `~: `~: `~: Cheri M. Hampton, Ph.D Howard Hughes Medical Institute Columbia University Medical Center 650 W 168th St. P&S Black 2-221 New York, NY 10032 (212)305-9524 ch2674(a)columbia.edu `~: `~: `~: `~: `~: `~: `~: `~: `~:

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Gap between C=O mainchain bond and supersmooth ribbon
by Dr. Jean-Didier Maréchal 09 Mar '09

09 Mar '09

Dear all, I want to represent the C=O bond that chelates an ion in my structure and the rest of the prot in ribbon (supersmooth). I don't want the carbon explicitly represented but yes the bond and the oxygen with a ball and stick representation. Following a previous post, I have two copies of my model. One is represented in ribbon. In the other one, I have the oxygen in bs and for the bond I did "bonddisplay always #1:22@C,O". It does pretty much what I want but I see that in many cases I have a empty gap between the end of the bond and the ribbon. Something I don't want. Is there a way to remove this gap? Or should I always represent the carbon also (something I find less esthetic that the other option). All the best, JD -----Mensaje original----- De: chimera-users-bounces(a)cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] En nombre de chimera-users-request(a)cgl.ucsf.edu Enviado el: viernes, 06 de marzo de 2009 5:16 Para: chimera-users(a)cgl.ucsf.edu Asunto: Chimera-users Digest, Vol 71, Issue 6 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. (no subject) (Du, Sean) 2. Re: (no subject) (Elaine Meng) 3. Re: (no subject) (Eric Pettersen) 4. Re: Issue with surface modelling using Chimera (Elaine Meng) 5. saving a rotated map (Scott Stagg) 6. Re: saving a rotated map (Gabriel Lander) ---------------------------------------------------------------------- Message: 1 Date: Thu, 5 Mar 2009 14:08:39 -0800 From: "Du, Sean" <Sean.Du(a)maxygen.com> Subject: [Chimera-users] (no subject) To: <chimera-users(a)cgl.ucsf.edu> Message-ID: <3A581C9EE7D7DF43ACE4FAA43592FAEC07B3542B(a)rc-ga-mail-1.mxygn.com> Content-Type: text/plain; charset="us-ascii" Dear Chimera developers and sophisticated users, I have trouble to show the surfaces of serveral crystal structures, including 1rzk and 2b4c. Whenever I select: Action/Surface/Show, I would get pop-up error window and the following message in my Reply Log: C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 Since I don't have problem with other pdb files, such as 3dnn, I wonder if this problem is simply associated with some particular pdb files? If anyone out there knows a few tricks to overcome this, I'd really appreciate it. Many thanks in advance, Sean ---------------------------------------------- Sean Du, Ph.D. Senior Scientist, Project Leader Maxygen, Inc. 515 Galveston Drive Redwood City, CA 94063 Office: (650) 298-5380 Cell: (510) 366-3586 -----------------------------------------------

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D-amino acids
by Francesco Pietra 06 Mar '09

06 Mar '09

Hi Elaine: As I was interested in inverting the configuration at the alph carbon of amino acids in a peptide, I came across (between ==) ========================= Elaine Meng meng at cgl.ucsf.edu Mon Jun 30 10:53:33 PDT 2008 Hi Yasser, Sorry, mutation with the Rotamers tool (or swapaa command) is only to L-amino acids. Some less convenient alternatives: - use Build Structure (under Tools... Structure Editing) to build out the D- side chain manually. Note the resulting bond lengths and angles are approximate. - open another structure that contains the D- amino acid, match the backbone atoms of the residue you wish to substitute, write out coordinates "relative to" the first structure, then manually edit the PDB file to substitute that sidechain for the one originally in the structure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 27, 2008, at 12:33 PM, Yasser Almeida Hernández wrote: > Can Chimera mutate by D-residues? If this is possible, how i can do > it? > > Thanks... > -- > Yasser Almeida Hernández > Estudiante, 4to Año Bioquímica > Facultad de Biología > Universidad de la Habana ================================ What about doing that with a molecular mechanics package? Most such packages have the capability of enantiomerize. Then, back to Chimera. Your view? thanks francesco pietra

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