[Chimera-users] Open Castp file in Chimera X
bixia.zhang at wsu.edu
Thu Apr 21 16:50:55 PDT 2022
Thank you Tom! I was always using Chimera and new to ChimeraX. I didn't know there is a separate user mailing list. I will keep that in mind next time.
From: Tom Goddard <goddard at sonic.net>
Sent: Thursday, April 21, 2022 4:48 PM
To: Zhang, Bixia <bixia.zhang at wsu.edu>
Cc: Chimera-users at cgl.ucsf.edu; ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Open Castp file in Chimera X
You will need to download the read_castp.py file from that web page. Then if it is your downloads directory you would use
In other words you have to tell it exactly where the file is unless it is in the directory where you downloaded the file. Also you can use the ChimeraX "cd" command to change to a new current directory in ChimeraX.
Best to email this question to the ChimeraX mailing list instead of the Chimera mailing list.
On Apr 21, 2022, at 4:42 PM, Zhang, Bixia via Chimera-users <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>> wrote:
I am trying to open .poc file from CASTP server in Chimera X. And I found this chimeraX recipehttps://rbvi.github.io/chimerax-recipes/castp/castp.html<https://urldefense.com/v3/__https:/rbvi.github.io/chimerax-recipes/castp/castp.html__;!!JmPEgBY0HMszNaDT!s8LfOHSQEc_nWpr4ho_FRyNSah1FZ9bSEqvGT687okU2j88l0GmtD8pL60cABtU8nxHoLsj948LIEYNlGWs$>. However, when I used the command open<help:user/commands/open.html> read_castp.py, it saidNo such file/path: read_castp.py. I am working on a Linux unbuntu box and I don't know if this is making any difference. Could you please help with this issue?
Thank you so much!
Read CASTP pockets file - ChimeraX Recipes<https://urldefense.com/v3/__https:/rbvi.github.io/chimerax-recipes/castp/castp.html__;!!JmPEgBY0HMszNaDT!s8LfOHSQEc_nWpr4ho_FRyNSah1FZ9bSEqvGT687okU2j88l0GmtD8pL60cABtU8nxHoLsj948LIEYNlGWs$>
We for the ChimeraX atom specifier from chain identifier, residue number and atom name. For example, the above lines are for atoms /A:45 at NH2, /B:27 at O, /B:27 at CG1 in ChimeraX syntax belonging to pockets 2, 1 and 1.
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