[Dock-fans] convert selected_clusters.pdb to selected_clusters.sph

Scott Brozell sbrozell at rci.rutgers.edu
Tue Oct 12 22:11:26 PDT 2010


Hi,

On Wed, Oct 06, 2010 at 12:35:04PM +0000, andrew_m_norris at talk21.com wrote:
> Hi dock-fans
>  I would like to select the clusters to be used in grid from showsphere i.e the largest ranked cluster in protein_clusters.sph (sphgen output) however the output from this is in pdb format. I need a top_rank_sphere.sph file as input for grid. 
> Is there any way to convert the top_ranked_cluster.pdb file from showspheres into top_ranked_cluster.sph or do i need to edit the protein_clusters.sph file generated in sphgen in some way. If this is the case could  someone suggest a way to go about it?
> 

I'm not sure that I understand your question, but the usual procedure is to
edit the sphgen output, apparently protein_clusters.sph in your case.
Note that showsphere is used just to visualize the sphgen output.
For the usual approach see 
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm

Perhaps your question is 'how to edit files in linux?'
See 'How to get started with Unix editors (vi)' in
http://www.osc.edu/supercomputing/training/bunix/
but gooogggllle will find lots more.

scott



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