[Chimera-users] Re: stereo viewing on Windows
Virginia B. Pett
pett at wooster.edu
Fri Sep 9 13:26:16 PDT 2005
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 at cgl.ucsf.edu wrote:
> Send Chimera-users mailing list submissions to
> chimera-users at 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 at cgl.ucsf.edu
>
> You can reach the person managing the list at
> chimera-users-owner at 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 at 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 at mail2.vcu.edu>
> Subject: [Chimera-users] creating a symmetric tetramer from a PDB file
> for a monomer?
> To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Message-ID: <200509061953.PAA18668 at 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 at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] creating a symmetric tetramer from a PDB
> file for a monomer?
> To: <gtseng at mail2.vcu.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <7485CA73-9B1A-492C-9F71-FB36FBF5B103 at 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 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 Sep 6, 2005, at 12:53 PM, <gtseng at 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 at 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 at eml-r.villa-bosch.de>
> Subject: [Chimera-users] Visualizing Electrostatic Potential of *.grd
> format?
> To: chimera-users at cgl.ucsf.edu
> Message-ID: <431ECB7D.8090203 at 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 at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Visualizing Electrostatic Potential of
> *.grd format?
> To: Anna Feldman-Salit <anna.feldman-salit at eml-r.villa-bosch.de>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <6902E794-4AAB-438D-A8D8-FB8E8849D7D6 at 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 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 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 at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>
>
> ------------------------------
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
> End of Chimera-users Digest, Vol 29, Issue 5
> ********************************************
More information about the Chimera-users
mailing list