[Dock-fans] segmentation fault - Dock3.5 Score in Dock6.2

John J. Irwin jji at cgl.ucsf.edu
Fri May 1 13:00:30 PDT 2009


Hi Barbara

We use filt in two different places in our standard protocol.
1. to trip very large proteins or protein complexes (e.g. the ribosome)
so that DOCK can focus on the relevant parts of a large complex
2. to select the region of the protein near the binding site for
surfacing by DMS to create a surface against which sphgen can run to
generate orientation spheres for docking.

For small proteins, or with manual curation, neither is strictly
necessary.  filt is necessary for automatic processing of large proteins
to remove distant parts that can be ignored so that the programs can run
and/or focus on the most important region of interest.

I hope this helps.

John


Collignon, Barbara C. wrote:
> Sorry, but I think I am confused. 
>
> I do not really understand what is the program FILT and in which case one has to use it ?
>
> Any explanations, please ?
>
> Barbara 
>
>
> -----Original Message-----
> From: dock-fans-bounces at docking.org on behalf of Collignon, Barbara C.
> Sent: Sat 4/25/2009 6:56 PM
> To: dock-fans at docking.org
> Subject: [Dock-fans] segmentation fault - Dock3.5 Score in Dock6.2
>  
>
> Hi everybody,
>
> I wonder whether one has to cut the protein before using the DOCK3.5 score with the DOCK6.2 version ? 
> I mean, should I select only the residues around the active site?
>
> In fact. With the DOCK3.5 version, some people used the FILT program to reduce the target before docking. 
>
> However, according to the DOCK6.2 tutorial, we don't have to select a small part of the protein only.
> But for the DOCK3.5 score maybe we should... 
>
> Any advices ?
>
> Barbara 
>
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