[Dockdev] write_orientations

Carlos P Sosa cpsosa at us.ibm.com
Thu Sep 18 19:17:40 PDT 2008

Per John's suggestion I am using this list, I am certainly willing to use 
any of these lists and contribute if I can.

Also related to conformers, Terry was kind enough to put together a small 
movie for us but never got info. how to generate the full ligands for a 
movie that shows the process of docking using DOCK6.  Any comments on this 
matter would also be appreciated.

I think that "if" enough info. is provided and not used as a default, most 
users are going to stay away from such a verbose option.  However, once 
you know what you'll get this info. is very useful.  Just by looking at 
the final anchor selected for growth, you immediately see why in some 
cases the wrong pose is predicted.

Scott Brozell <sbrozell at scripps.edu>
Carlos P Sosa <cpsosa at msi.umn.edu>
Dockdev at docking.org
09/18/2008 06:38 PM
Re: [Dockdev] write_orientations


My preference is to send these operational questions to dock-fans
in the hope that someone besides John or me will answer them.
By the way, I invite comments on ways to foster more user
participation on answering dock-fans.

ECho, Echo, echo.

I recall conversations with Terry, where writing growth was discussed;
I think the concensus was that this would just blow up in the hands 
of users due to the multiplicative file size growth.
But I think she did emit such info during her pruning algorithm 
studies.  You should seek out the great east bay oracle
(and follow up with a summary here).

Ok, so this one might have a development aspect.


Where does a pirate dock his ship ?

On Thu, 18 Sep 2008, Carlos P Sosa wrote:

> Activating these two flags create a mol2 file with only info. about the
> anchor.  Is there a way to get anchor plus more layers?
> write_orientations                                           no
> num_scored_conformers_written                                1

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