hello Blaine,
Thank you very much for your response!
sorry I did not explain my problem correctly, in fact after splitting
of the state I could see all states as the separate models. The
problem is only in the multi-model pdb that I obtained from DGL file
of autodock (which normally contains only the coordinates for
ligand!). I converted this file to PDB obtaining the correct
multi-model PDB of the ligand but then just cut it with the
receptor.pdb. So eventually I have the protein only within the first
frame. What I am looking for to fuse protein.pdb with EACH of the
model of the ligand. Probably we can do it via Pymol, starting from 2
pdbs: 1) multi-model pdb of the ligand (e.g. with 20 models) and 2)
receptor.pdb with 1 model of protein. There is no problem with
superimposition of both, I need just to save it correctly in a
multi-model file to see 20 frames containing both protein and ligand.
Cheers,
J.
чт, 15 окт. 2020 г. в 11:05, Mooers, Blaine H.M. (HSC)
<blaine-moo...@ouhsc.edu>:
>
> Hi Jeff,
>
> I would se the pdb file 1nmr as a template to reformat your file accordingly:
> fetch 1nmr, type=pdb.
> Open it with a text editor
> You will see the that END is used only once, at the every bottom of the file
> after the last model.
> This is why you are not seeing multiple models with all_states.
>
> You need to end the protein model with TER and then ENDMDL and start the
> ligand with 'MODEL 2'
>
> TER 1291 VAL A 85
> ENDMDL
> MODEL 2
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
> ________________________________________
> From: Jeff Saxon [jmsstarli...@gmail.com]
> Sent: Thursday, October 15, 2020 2:34 AM
> To: pymol-users
> Subject: [EXTERNAL] [PyMOL] Protein-ligand multi-model pdb extracted from
> docking
>
> Hello there.
>
> I am dealing with the extraction of ligand coordinates (in PDB) from
> the typical autodock output file (DLG). Using simple shell routine I
> can do it in just few steps:
>
> # convert DLG to PDBQT
> grep '^DOCKED' test.dlg | cut -c9- > ${output}/test.pdbqt
> # convert PDBQT to PDB
> cut -c-66 ${output}/test.pdbqt > ${output}/test.pdb
> # take pdb of the receptor protein (used for this docking!) and add
> it to the ligand ensemble
> cat receptor.pdb ${output}/test.pdb | grep -v '^END ' | grep -v
> '^END$' > ${output}/complex_test.pdb
>
> The problem of this routine is in the last step when I add the
> receptor pdb to the ligand ensemble - it actually creates multi-model
> pdb (nmr like format) where the receptor is present only in the first
> model (and the ligands in the rest). So I can not examine in PyMol
> protein-ligand interactions (only even if I use split_states to
> separate all models).
>
> Could someone suggest a modification of my shell routine capable of
> adding a receptor.pdb to each of the ligand models (thus obtaining
> complex in proper multi-model format similar to NMR structure or
> molecular dynamics trajectory)?
>
> Thanks!!
> J.
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=xCGrlhjwjhsbR-Y2YVa0DFXKZvcilxJrcaqrg65I7VA&s=DY9b89ABzFLCckLkueYmyFS4qox8Us86lsJvBSl5brY&e=
> Unsubscribe:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=xCGrlhjwjhsbR-Y2YVa0DFXKZvcilxJrcaqrg65I7VA&s=BiQJgzsCAIbfbXofwH-1shmIvOUGyci3RDe8dVR6V0I&e=
_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe:
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
