Re: [PyMOL] how to create multi-model pdb for protein-ligand complex?

[Enrico M. <jms...@gm...>]

try this man!

awk 'NR==FNR {s = s $0 ORS; next} $0 == "ENDMDL" {$0 = s $0} 1'
./receptor.pdb ./docking.pdb >> together.pdb

пт, 7 янв. 2022 г. в 18:10, Saurabh Gayali <sau...@gm...>:

> I guess we need to split the docking poses first and then merge them
> together.
> Hope I come up with a python script or anyone else does.
>
> On Fri, 7 Jan, 2022, 18:47 Enrico Martinez, <jms...@gm...>
> wrote:
>
>> In the case of
>> cmd.save("together.pdb", "all", "0", "pdb")
>> it saves everything in one pdb when the protein is present only in the
>> first model, while I need to obtain its representation in all models
>> Cheers
>> E.
>>
>> пт, 7 янв. 2022 г. в 13:14, Saurabh Gayali <sau...@gm...>:
>>
>>> Have you tried the save command after opening both files?
>>> https://pymol.org/dokuwiki/doku.php?id=command:save
>>> Though not sure how the different poses will merge.
>>> Also looking for a solution for a similar problem.
>>>
>>> ------------------------------
>>>
>>> *Saurabh Gayali* / Post Doctoral Fellow
>>> sau...@gm... / +91 8800412916
>>>
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>>> On Fri, Jan 7, 2022 at 3:43 PM Enrico Martinez <jms...@gm...>
>>> wrote:
>>>
>>>> Dear Autodock Users!
>>>> I am dealing with the structural analysis of the protein-ligand
>>>> interactions observed in the protein-ligand docking using VINA.
>>>> Basically operating with the outputs I have two different pdb files:
>>>> 1) for docking receptor (1 protein model) as well as for 2) docking
>>>> sollutions (100 solutions). So I use pymol to open the both filles and
>>>> visualize them
>>>>
>>>> pymol sollutions.pdb receptor.pdb
>>>>
>>>> May you suggest me some pymol command to merge the both in the pymol
>>>> to. create multi-model PDB consisted of the both receptor and ligand
>>>> poses in order then I could perform some structural analysis of this
>>>> combined complex?
>>>> Many thanks in advance
>>>> Enrico
>>>>
>>>>
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>>>