Menu
▾
▴
Re: [PyMOL] surface representation of the protein-ligand interactions
|
From: Enrico M. <jms...@gm...> - 2022-01-10 16:37:03
|
Right, thank you, Blaine!
It works very well now! Actually there was a problem in the selection
from my part so..
I will play with the surfaces a little bit and then will update this
topic with my questions :-)
Cheers,
Enrico
пн, 10 янв. 2022 г. в 16:25, Mooers, Blaine H.M. (HSC)
<Bla...@ou...>:
>
> Hi Enrico,
>
> You do not need the first line of your script.
>
> This one-liner worked for me in the terminal.
>
> pymol -c -d "cmd.fetch('3nd3');cmd.show('surface');cmd.set('transparency','0.5');cmd.save('surf.pse');cmd.png('surf.png')"
>
> You might test reversing the order of the cmd.png() and cmd.save() commands.
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology, College of Medicine
> Director of the Laboratory of Biomolecular Structure and Function
> Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
> Full Member, Cancer Biology Program, Stephenson Cancer Center
> University of Oklahoma Health Sciences Center
>
> Mailing Address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> Office: 405-271-8300 Lab: 405-271-8312
>
> Websites:
> Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
> BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
> COBRE in Structural Biology: https://www.ou.edu/structuralbiology
> ________________________________________
> From: Ali Saad Kusay via PyMOL-users [pym...@li...]
> Sent: Monday, January 10, 2022 8:48 AM
> To: Enrico Martinez
> Cc: pymol-users
> Subject: [EXTERNAL] Re: [PyMOL] surface representation of the protein-ligand interactions
>
> Hi Enrico,
>
> This is beyond my understanding, try and run this bash script without making the surface transparent (to figure out if the issue comes from the transparency)
>
> Also try the rebuild command before saving the image: https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Rebuild&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=QM8ZtM6vxjrnYB0Cs6BSV-M8WweuPuuTS1xLMGYQdKU&e=
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
> On 10/1/22, 11:10 pm, "Enrico Martinez" <jms...@gm...> wrote:
>
> Thank you very much,Ali!
> just one question: when I do the surface calculations using bash
> script operating with the command lines of the pymol it produces
> correctly pse session with the surfaces. BUT if I save an image using
> png, the surface is totally absent. Here are my commands directly from
> the shell script:
>
> $pymol -c -d "
> from pymol import cmd
> cmd.load('${results}/${output}_${lig_name}_${receptor}_rep${i}.pdb')
> cmd.show( 'surface', '${output}* and polymer within 15 of ${output}*
> and not polymer' )
> cmd.set( 'transparency', '0.5' )
> cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
> cmd.png('${vizu}/${output}_${lig_name}_rep${i}.png',width=${image},height=${image},dpi=50,ray=0)
> "
> As the result of this workflow, the surface is present in the PSE
> file but not in the png image. Otherwise when I save png directly from
> the pymol's GUI the surface is well captured on the png as well. What
> should I include in my script ?
>
> пн, 10 янв. 2022 г. в 12:18, Ali Saad Kusay <aku...@un...>:
> >
> > Hi Enrico,
> >
> > You can carve the protein surface around the ligand, i.e. show only the surface behind the ligand, see this guide: https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_1Of6CNLJyQU0W9yVofmRSV0-3Fdomain-3Dpymol.org&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=eU60ct3XrRn6e7JdG6JrHLyikGkuUbzJY35JQFXvTv8&e=
> >
> > You can also try and made the surface more transparent, but this doesn't always give the best results, see: https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_vdsUCOMKzVTp8wQ53fvOudq-3Fdomain-3Dpymolwiki.org&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=pOFWGOP750OszaW7BCL8qGLr_VvBCCumHmvodMSYBeo&e= , i.e.:
> >
> > set transparency, 0.5
> >
> > It would help to see an image of what you are working with atm
> >
> > Cheers,
> >
> > Ali
> >
> > Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> > The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> > 424, Brain and Mind Centre | The University of Sydney | NSW 2050
> >
> >
> > On 10/1/22, 10:10 pm, "Enrico Martinez" <jms...@gm...> wrote:
> >
> > Dear Pymol users!
> > Working on the vizualisation of the protein-ligand interactions I
> > would like to switch from cartoon to the surface representation of the
> > protein, while still being capable to see the ligand-binding cavity
> > (as well as non-covalent interactions)
> >
> > Could you suggest me some combination of the options which could helps
> > me with such vizualisaiton?
> > I have alread tried
> > show surface, all within 5 of my_pdb and not polymer
> > set surface_smooth_edges, onset surface_smooth_edges, on
> > where my_pdb and not polymer corresponds to the selection of the ligand
> >
> > Eventualy this create cool surface representation of the protein and
> > but completely hides the ligand-binding cavity
> > Many thanks in advance!
> > Enrico
> >
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_5uDYCP7LAXfKwZVvQF1Df45-3Fdomain-3Dmail-2Darchive.com&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=f6UjxY4QYDP77HQZ2CqSwjcwA_HDNuyv4cn6nskHIq0&e=
> > Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_Q3GJCQnMBZfkQ9ZB7FkIfVr-3Fdomain-3Dsourceforge.net&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=lxdjMlSEnLEry730CbGSXWOU9HvpC8iBFjlmcWohToU&e=
> >
> >
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=jECdW3kdL8QeZ4l5PxiMhbpjSJBrXPLt0KPxa2kpcwI&e=
> Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=LFkputyTYxDqA2BAGoUDzxEwKZsm3odkMNEHWVV7IZg&e=
|
