[Dock-fans] sphgen command, generating spheres
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
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.
UCSF Computer Graphics Lab
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:
> 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
> 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!
> Dock-fans mailing list
> Dock-fans at docking.org
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