Dear Amna (?),


2012/11/12 amna khan <amnakhan369@gmail.com>
i have docked ligand with protein and final docked protein containing ligand conformation have been generated into one file. Now for this docked ligand-protein structure i want to calculate the electron dennsity map by pymol.
 

If I understand correctly, what you are doing does not make any sense (I am a protein crystallographer...)

To the best of my knowledge, what you are trying to do is not possible.

With best intentions,

Folmer

 


On Sun, Nov 11, 2012 at 5:22 PM, Folmer Fredslund <folmerf@gmail.com> wrote:
Dear Amna (?),


2012/11/11 amna khan <amnakhan369@gmail.com>
hi,
 
i want to calculate the electron density maps for my docked protein from autodock4.2, when i load. fld.maps file generated by autodock and my docked protein at same time , no maps are generated.


1. electron density maps are calculated from experimental data and model phases. No computer program will ever give you any (real) electron density. I think you are confusing the terms here.

2. Are you trying to dock a ligand, or dock two proteins together?  There is a very nice plugin (http://www.pymolwiki.org/index.php/Autodock_plugin) by Daniel Seeliger. I would use that.

Hope this helps

Folmer Fredslund





 
 
please help
 
regards

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Folmer Fredslund





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Folmer Fredslund