[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


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 

Perhaps your question is 'how to edit files in linux?'
See 'How to get started with Unix editors (vi)' in
but gooogggllle will find lots more.


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