Re: [PyMOL] surface representation of the protein-ligand interactions

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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
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________________________________________
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
    >
    >
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Re: [PyMOL] surface representation of the protein-ligand interactions

PyMOL is an OpenGL based molecular visualization system

Re: [PyMOL] surface representation of the protein-ligand interactions