September 2005 - Chimera-users - RBVI Mailing Lists

Re: stereo viewing on Windows
by Virginia B. Pett 09 Sep '05

09 Sep '05

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(a)cgl.ucsf.edu wrote: > 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. creating a symmetric tetramer from a PDB file for a monomer? > (gtseng(a)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) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 06 Sep 2005 15:53:41 -0400 > From: <gtseng(a)mail2.vcu.edu> > Subject: [Chimera-users] creating a symmetric tetramer from a PDB file > for a monomer? > To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <200509061953.PAA18668(a)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 > > ------------------------------ > > Message: 2 > Date: Tue, 6 Sep 2005 13:48:50 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] creating a symmetric tetramer from a PDB > file for a monomer? > To: <gtseng(a)mail2.vcu.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <7485CA73-9B1A-492C-9F71-FB36FBF5B103(a)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(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 Sep 6, 2005, at 12:53 PM, <gtseng(a)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(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > > ------------------------------ > > Message: 3 > Date: Wed, 07 Sep 2005 13:14:05 +0200 > From: Anna Feldman-Salit <anna.feldman-salit(a)eml-r.villa-bosch.de> > Subject: [Chimera-users] Visualizing Electrostatic Potential of *.grd > format? > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <431ECB7D.8090203(a)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. > > ------------------------------ > > Message: 4 > Date: Wed, 7 Sep 2005 09:16:40 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Visualizing Electrostatic Potential of > *.grd format? > To: Anna Feldman-Salit <anna.feldman-salit(a)eml-r.villa-bosch.de> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <6902E794-4AAB-438D-A8D8-FB8E8849D7D6(a)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(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 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(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 29, Issue 5 > ********************************************

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Rotation Angle
by Huang, Zhong 07 Sep '05

07 Sep '05

Hi, dear chimera developers' I am a Chimera user of UT Medical school at Houston . Here I want to know how chimera rotates the loading structure. I wish to know what the rotation parameters mean? Which coordinate sysmtem they refere to? I check the on-line tutorial. Unfortunately, I didn't get the answer. Best Zhong Huantg

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[Chimera-users] Visualizing Electrostatic Potential of *.grd format?
by Anna Feldman-Salit 07 Sep '05

07 Sep '05

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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Suggestion re Docking Results
by Philip Crawford 06 Sep '05

06 Sep '05

Hi. I like Chimera and hit a limit yesterday. (Windows version.) We are running DOCK using the ZINC databases, which produces very large output_scored.mol2 files. I tried using Chimera to open and sort one of these. After an hour, I killed Chimera. John Irwin suggested (via the Dock-fans list) that I recommend you set a limit on the size of output file to be opened. An alternative may be to set a limit on the number of records which will be read, regardless of file size. Thanks for a useful product. Cheers, Philip Crawford __________________________________________________ Philip Crawford, B. Comp. Sc., MIEEE Structural BioInformatics and Drug Design Group http://www.sbio.med.unsw.edu.au/sbio School of Medical Sciences The University of NSW Phone: +61-2-9385 2564 Mobile: +61-419-294 698 Fax: +61-2-9385 1059 Email: <mailto:p.crawford@unsw.edu.au> p.crawford(a)unsw.edu.au __________________________________________________

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changing the rendering of distanced dotted lines
by Boaz Shaanan 06 Sep '05

06 Sep '05

Hi, Distances between pairs of atoms are marked as dotted lines by the 'distances' panel. Is it possible to make those dots bigger by scaling them up somehow so that they are seen more clearly ? They obviously get larger when I zoom in but sometimes I'd rather stay in the zoom-out view but make the dots more visible. Please let me know. Thanks, Boaz

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[Chimera-users] Save pdb files only have 5 subunits at 5-fold at virus?
by Jason 04 Sep '05

04 Sep '05

Hi all Is it possible to save pdb files that only have 5 subunits at 5-fold after using mulitscale tools buliding virus paritle. And this pdb file can open at other programs too, ex: DeepView, PyMOL. When I use File/Save PDB chimera can save pdb file, but this file(model) only can show correctly at chinera. If I opened this file at PyMOL or DeepViewit only show the origional 3(A, B, C)chain model thanks Jason

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