[Dock-fans] sphgen command, generating spheres

Eric Pettersen pett at cgl.ucsf.edu
Wed Jun 3 13:21:45 PDT 2009


It turns out that there's an issue on Windows in that the Write DMS  
tool outputs Windows-style line endings (i.e. a carrriage-return  
character followed by a new-line character) whereas sphgen only  
properly handles Unix-style line endings (i.e. just a new-line  
character).

So, as of a few minutes ago there is a new version of Chimera  
available that always outputs Unix-style line endings for DMS files  
regardless of what platform Chimera is running on.  You get it by  
going to the Chimera home page (http://www.cgl.ucsf.edu/chimera/) and  
following the "Daily Builds" link.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


On Jun 3, 2009, at 9:28 AM, Sudipto Mukherjee wrote:

> Dear Hannah,
>
> You can create an input file contains answers to all the questions  
> sphgen asks. Then you can run sphgen as:
> sphgen -i INSPH -o OUTSPH
> where INSPH is a text input file. Here is a sample input file I use:
>
> receptor.ms
> R
> X
> 0.0
> 4.0
> 1.4
> receptor.sph
> where receptor.ms is the molecular surface generated. Normally I use  
> the stand-alone dms tool, but the Write DMS tool in chimera works  
> just the same. Sample files from http://ringo.ams.sunysb.edu/index.php/2008_DOCK_tutorial_with_1LAH
>
> Regards
> Sudipto Mukherjee
> Graduate Student, Robert C. Rizzo Lab
> Dept. of Applied Math & Statistics, Stony Brook University
>
> From: hannah pamela tan <hpdiamantetan at yahoo.com>
> To: dock <dock-fans at docking.org>
> Sent: Wednesday, June 3, 2009 4:00:37 AM
> Subject: [Dock-fans] sphgen command, generating spheres
>
> Dear Sir,
>
> i'm sorry to ask this question but i really don't have an idea where  
> to apply or execute the sphgen command. i can't fully understand the  
> steps in the dock tutorials. i tried it on the cygwin terminal but  
> it ended up in an error.
>
> i have already installed the dock 6.2 and i have also prepared the  
> ligands and macromolecules to be used (as was instructed in the  
> tutorials).. and i already used the Write DMS tool in the Chimera.
>
> can i please help me on what to do next? thank you!
>
>
> Hannah Tan
> _______________________________________
> Smile!  Jesus loves yah!
>
>
> _______________________________________________
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> Dock-fans at docking.org
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