Dear Amna (?),

2012/11/12 amna khan <>
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,



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

2012/11/11 amna khan <>
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 ( by Daniel Seeliger. I would use that.

Hope this helps

Folmer Fredslund

please help

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Folmer Fredslund

Folmer Fredslund