[chimerax-users] Analysis of docking results

[Luigi Marongiu]

Thank you! I'll try Chimera.
Best wishes for Merry Christmas,
Luigi
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, December 14, 2022 20:05
To: Luigi Marongiu <luigi.marongiu at outlook.com>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Analysis of docking results

Hi Luigi,
(1) if the structure really does have chains B and C, the other chains should also be in the same menu (Select... Chains).

(2) Sorry, but ChimeraX's ViewDockX tool does not read SwissDock output currently. For easily looking through the docked ligands one by one and seeing their scores, you would still need to use the ViewDock tool in Chimera (not ChimeraX).

There is a ticket open to make ViewDockX/ChimeraX understand SwissDock output, but we have not had time to work on that yet:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4232>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Dec 14, 2022, at 3:02 AM, Luigi Marongiu via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> Dear sir or madam,
> I am new to docking analysis.
> I obtained a model from SwissDock but there are some commands that do not work on ChimeraX.
>        • I can load the molecule, which is composed by 4 homo-chains. I can select one chain (A); how can I delete or hide chains B-D. I can select chain A using select>chain​`; is there a way to hide the others?
>        • The model (saved in the file clusters.dock4.pdb) shows several ligands:
> <Screenshot from 2022-12-14 11-54-50.png><Outlook-hkjqyk44.png>
> Is there a way to show only the ligands with the highest docking score?
> 3. the tools>binding analysis>ViewDockX​` says that "No suitable models found for ViewDockX". But is not this the "clusters.dock4.pdb"? How can I load the model into ChimeraX?
> Thank you.
> Best regards,
> Luigi Marongiu
> Ph.D., B.Sc. (Hons.)

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