Open Castp file in Chimera X
Good afternoon, I am trying to open .poc file from CASTP server in Chimera X. And I found this chimeraX recipe https://rbvi.github.io/chimerax-recipes/castp/castp.html. However, when I used the command open<help:user/commands/open.html> read_castp.py, it said No 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! Best, Bixia Read CASTP pockets file - ChimeraX Recipes<https://rbvi.github.io/chimerax-recipes/castp/castp.html> We for the ChimeraX atom specifier from chain identifier, residue number and atom name. For example, the above lines are for atoms /A:45@NH2, /B:27@O, /B:27@CG1 in ChimeraX syntax belonging to pockets 2, 1 and 1. rbvi.github.io
Hi Bixia, You will need to download the read_castp.py file from that web page. Then if it is your downloads directory you would use open ~/Downloads/read_castp.py 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. Tom
On Apr 21, 2022, at 4:42 PM, Zhang, Bixia via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Good afternoon, 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://rbvi.github.io/chimerax-recipes/castp/castp.html>. 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! Best, Bixia
Read CASTP pockets file - ChimeraX Recipes <https://rbvi.github.io/chimerax-recipes/castp/castp.html> We for the ChimeraX atom specifier from chain identifier, residue number and atom name. For example, the above lines are for atoms /A:45@NH2, /B:27@O, /B:27@CG1 in ChimeraX syntax belonging to pockets 2, 1 and 1. rbvi.github.io <http://rbvi.github.io/> _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>
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. Bixia From: Tom Goddard <goddard@sonic.net> Sent: Thursday, April 21, 2022 4:48 PM To: Zhang, Bixia <bixia.zhang@wsu.edu> Cc: Chimera-users@cgl.ucsf.edu; ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Open Castp file in Chimera X Hi Bixia, You will need to download the read_castp.py file from that web page. Then if it is your downloads directory you would use open ~/Downloads/read_castp.py 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. Tom On Apr 21, 2022, at 4:42 PM, Zhang, Bixia via Chimera-users <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> wrote: Good afternoon, 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$>. However, when I used the command open<help:user/commands/open.html> read_castp.py, it saidNo such file/path: read_castp.py. I am working on a Linux unbuntu box and I don't know if this is making any difference. Could you please help with this issue? Thank you so much! Best, Bixia Read CASTP pockets file - ChimeraX Recipes<https://urldefense.com/v3/__https:/rbvi.github.io/chimerax-recipes/castp/castp.html__;!!JmPEgBY0HMszNaDT!s8LfOHSQEc_nWpr4ho_FRyNSah1FZ9bSEqvGT687okU2j88l0GmtD8pL60cABtU8nxHoLsj948LIEYNlGWs$> We for the ChimeraX atom specifier from chain identifier, residue number and atom name. For example, the above lines are for atoms /A:45@NH2, /B:27@O, /B:27@CG1 in ChimeraX syntax belonging to pockets 2, 1 and 1. rbvi.github.io<https://urldefense.com/v3/__http:/rbvi.github.io/__;!!JmPEgBY0HMszNaDT!s8LfOHSQEc_nWpr4ho_FRyNSah1FZ9bSEqvGT687okU2j88l0GmtD8pL60cABtU8nxHoLsj948LIWvjiJOo$> _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users<https://urldefense.com/v3/__https:/www.rbvi.ucsf.edu/mailman/listinfo/chimera-users__;!!JmPEgBY0HMszNaDT!s8LfOHSQEc_nWpr4ho_FRyNSah1FZ9bSEqvGT687okU2j88l0GmtD8pL60cABtU8nxHoLsj948LIbu-CX5c$>
participants (2)
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Tom Goddard -
Zhang, Bixia