We have windows XP machine in one of our labs. The machine is running chimera. We want to run chimera in stereo mode on this machine. as per the documentation, create a shortcut of chimera on the desktop and then append "--stereo" options in target mode. But target mode does not recognize this. Which file helps start the stereo mode on windows machine, so that i can put that file path in target? ________________________________________ Virginia B. Pett Professor of Chemistry Department of Chemistry, The College of Wooster 943 College Mall, Wooster, OH 44691 Telephone: 330-263-2114 Fax: 330-263-2386 On Sep 7, 2005, at 3:00 PM, chimera-users-request@cgl.ucsf.edu wrote:
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Today's Topics:
1. creating a symmetric tetramer from a PDB file for a monomer? (gtseng@mail2.vcu.edu) 2. Re: creating a symmetric tetramer from a PDB file for a monomer? (Elaine Meng) 3. Visualizing Electrostatic Potential of *.grd format? (Anna Feldman-Salit) 4. Re: Visualizing Electrostatic Potential of *.grd format? (Elaine Meng)
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Message: 1 Date: Tue, 06 Sep 2005 15:53:41 -0400 From: <gtseng@mail2.vcu.edu> Subject: [Chimera-users] creating a symmetric tetramer from a PDB file for a monomer? To: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Message-ID: <200509061953.PAA18668@despina.vcu.edu> Content-Type: text/plain; charset=iso-8859-1
Dear Chimera creators: Could you please let me know whether it is possible to create a tetramer structure with 4-fold symmetry from a PDB file for a monomer? Specifically, I want to create a structure of a voltage-gated K channel which has 4 monomers surrounding a central pore symmetrically, beginning with the PDB file for a monomer. There is no 'transformation matrix' in the PDB file to allow me to create the tetramer easily. Thank you very much for your help!
Gea-Ny Tseng
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Message: 2 Date: Tue, 6 Sep 2005 13:48:50 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] creating a symmetric tetramer from a PDB file for a monomer? To: <gtseng@mail2.vcu.edu> Cc: chimera-users@cgl.ucsf.edu Message-ID: <7485CA73-9B1A-492C-9F71-FB36FBF5B103@cgl.ucsf.edu> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
Hello Gea-Ny, The Chimera features that generate multimers (the tools Unit Cell and Multiscale Models) all use matrix information in the PDB file. Multiscale Models uses BIOMT, MTRIX, SMTRY, and/or CRYST1 records, and Unit Cell uses MTRIX, SMTRY, and/or CRYST1.
It sounds like you don't have any of those in your PDB file.
You could either (A) figure out what information should be in such a matrix line and edit it into your file before using one of the Chimera tools, or (B) open four copies of your monomer and try to position them by hand. If you know what the axis of rotation should be, you can use Constrained Move (Tools... Movement... Constrained Move in recent versions) to define and use an axis of rotation. http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/ constrained/constrained.html
Neither of these is very easy, but I don't know of any way to automatically position the monomers without the matrix information. It sounds like BIOMT (REMARK 350) records would be the most appropriate. Even with an appropriate example, you would still have to change the values.
REMARK 350 is described at the PDB web site (you have to scroll down to get to the description of REMARK 350): http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_31.html
Here is an example from 1fav (threefold): REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 35.81900 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 17.90950 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 31.02016 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@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 Sep 6, 2005, at 12:53 PM, <gtseng@mail2.vcu.edu> wrote:
Dear Chimera creators: Could you please let me know whether it is possible to create a tetramer structure with 4-fold symmetry from a PDB file for a monomer? Specifically, I want to create a structure of a voltage-gated K channel which has 4 monomers surrounding a central pore symmetrically, beginning with the PDB file for a monomer. There is no 'transformation matrix' in the PDB file to allow me to create the tetramer easily. Thank you very much for your help!
Gea-Ny Tseng _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Message: 3 Date: Wed, 07 Sep 2005 13:14:05 +0200 From: Anna Feldman-Salit <anna.feldman-salit@eml-r.villa-bosch.de> Subject: [Chimera-users] Visualizing Electrostatic Potential of *.grd format? To: chimera-users@cgl.ucsf.edu Message-ID: <431ECB7D.8090203@eml-r.villa-bosch.de> Content-Type: text/plain; charset=us-ascii; format=flowed
Dear All,
I would like to ask you a question regarding the visualization of electrostatic potential on msms. For this purpose, of course, I need a readable format for Potential Map. In the past I used to work with DelPhi for potential calculations and then visualize the outputted *.14 file by Chimera. Today I calculate potentials by using UHBD program, while output files are saved in /phi/ format with .grd extension (could be written either in binary or ascii form). Unfortunately, the Chimera doesn't recognize this format.
Dear Chimera users, do you know the way to convert the *.grd files to the *.phi ones readable by Chimera, or any other trick? I can't recalculate the potentials by DelPhiController, because I have only one dat-file for both radii sizes and charges (it also doesn't work in the simple way).
I'd very appreciate any help of yours!
Yours sincerely,
Anna.
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Message: 4 Date: Wed, 7 Sep 2005 09:16:40 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] Visualizing Electrostatic Potential of *.grd format? To: Anna Feldman-Salit <anna.feldman-salit@eml-r.villa-bosch.de> Cc: chimera-users@cgl.ucsf.edu Message-ID: <6902E794-4AAB-438D-A8D8-FB8E8849D7D6@cgl.ucsf.edu> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
Hi Anna, Actually, Chimera does read UHBD grids, the binary version. The older approach to displaying potential on a surface, DelPhiViewer, is being phased out in favor of the newer and more general tool, Surface Color (Tools... Surface/Binding Analysis... Electrostatic Surface Coloring or Tools... Volume Data... Surface Color both open this tool).
Surface Color can color surfaces based on any of the volume data (3D grid) formats that can be read by Volume Viewer (which include UHBD binary): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/ volumeviewer.html#formats
Surface Color is relatively new. It is available in the snapshots 1.2154 (linux, mac) and 1.2143 (windows). It is also available in 1.2105, but I don't recommend using that one because we have made it easier to use in the more recent snapshots. Here is the man page for Surface Color in version 1.2154: http://www.cgl.ucsf.edu/chimera/1.2154/docs/ContributedSoftware/ surfcolor/surfcolor.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@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 Sep 7, 2005, at 4:14 AM, Anna Feldman-Salit wrote:
Dear All,
I would like to ask you a question regarding the visualization of electrostatic potential on msms. For this purpose, of course, I need a readable format for Potential Map. In the past I used to work with DelPhi for potential calculations and then visualize the outputted *.14 file by Chimera. Today I calculate potentials by using UHBD program, while output files are saved in /phi/ format with .grd extension (could be written either in binary or ascii form). Unfortunately, the Chimera doesn't recognize this format.
Dear Chimera users, do you know the way to convert the *.grd files to the *.phi ones readable by Chimera, or any other trick? I can't recalculate the potentials by DelPhiController, because I have only one dat-file for both radii sizes and charges (it also doesn't work in the simple way).
I'd very appreciate any help of yours!
Yours sincerely,
Anna. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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End of Chimera-users Digest, Vol 29, Issue 5 ********************************************