[Dock-fans] showsphere

Trent E. Balius tbalius at aol.com
Thu Nov 8 07:36:02 PST 2012


Hi Calvin,


I believe that following
  Enter name of sphere cluster file:
      sphgen_cluster.in

should be something like this

  Enter name of sphere cluster file:
    1DF8.receptor.sph

Note that the sphere cluster file should be the file generated from sphgen and have the extension .sph.

See the tutorial:

http://ringo.ams.sunysb.edu/index.php/2012_DOCK_tutorial_with_Streptavidin

excerpt from the tutorial

  In order to visualize the generated spheres, you can use a program called showsphere. Showsphere is an interactive program. In the command line, simply type

  showsphere

  You will be asked the following questions:

  Enter name of sphere cluster file:
    1DF8.receptor.sph
  Enter cluster number to process (<0 = all): -1
  Generate surfaces as well as pdb files (<N>/Y)? N
  Enter name for output file prefix:
    1DF8.output.
  Process cluster 0 (contains ALL spheres) (<N>/Y)? N

  In this case, 28 pdb files should be generated.

  An alternative way to do this is to create an input file, showsphere.in, as follows:

  1DF8.receptor.sph
  -1
  N
  1DF8.output
  N

  Then type the command showsphere

  showshpere < showsphere.in

I hope that this helps,

Trent

 

======================================
Trent E. Balius, PhD
Shoichet Lab – Dept. of Pharm Chem 
           1700 4th Street
           Box 2550
           San Francisco, CA 94158     
Office: Byers Hall, Rm 509
URL: http://docking.org/~tbalius
======================================

 

 

-----Original Message-----
From: Calvin F. Cahall <calvin.cahall at centre.edu>
To: dock-fans <dock-fans at docking.org>
Sent: Thu, Nov 8, 2012 7:22 am
Subject: [Dock-fans] showsphere


Hello,

I am having problems with the "showsphere" command working through sphere 
generation dock tutorial. After using the "sphgen" command to create the OUTSPH 
and rec.sph files, I then tried this.
$ showsphere
 Enter name of sphere cluster file:
sphgen_cluster.in
 Enter cluster number to process (<0 = all): 1
 Generate surfaces as well as pdb files (<N>/Y)? Y
 Enter name for output PDB file name:
sphgen_cluster.pdb
 Enter name for output surface file name:
sphgen_cluster.out

 Error!  Cluster not found: 1

I read an email of someone having the same problem and the suggestion was to 
check the rec.sph file to ensure that the cluster name was indeed "1". I have 
done so as well as checked to be sure that my rec.sph file is that same as in 
the tutorial, which was another suggestion.
Any help would be great!

Calvin
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