Dear Sir
Recently I can not use the ChimerX to do the alphafold prediction. The error message is some connection to the colab is broken sine March 2024. I am wondering when this feature of ChimeraX will come back?
Thank you
Ju-Fang
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Dear all,
May I save in a file the residues colored by the Select Zone command?
Best,
Marco
Hi Marco, There is an option when saving PDB to save only the currently selected atoms.
In the dialog from menu: File... Save, if you choose "Files of type:" to be "PDB" then you can check the option "Save selected atoms only"
Or, you can use the "save" command with "selectedOnly true" https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb
You may know this part already: If you want only whole residues instead of just atoms in the zone that could be fragments of residues, then choose the "residues" option in the dialog from menu: Select... Zone, or use the "select zone" command with "residues true" or use the command-line residue zone specifier, e.g.
select ligand :<4.5 & protein
... as explained https://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html#zone https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 6, 2024, at 4:06 AM, Marco Sette via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear all, May I save in a file the residues colored by the Select Zone command? Best, Marco
Thanks Elaine,
that's perfect!
Best,
Marco
Il 06/05/24 20:42, Elaine Meng ha scritto:
Hi Marco, There is an option when saving PDB to save only the currently selected atoms.
In the dialog from menu: File... Save, if you choose "Files of type:" to be "PDB" then you can check the option "Save selected atoms only"
Or, you can use the "save" command with "selectedOnly true" https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb
You may know this part already: If you want only whole residues instead of just atoms in the zone that could be fragments of residues, then choose the "residues" option in the dialog from menu: Select... Zone, or use the "select zone" command with "residues true" or use the command-line residue zone specifier, e.g.
select ligand :<4.5 & protein
... as explained https://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html#zone https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 6, 2024, at 4:06 AM, Marco Sette via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear all, May I save in a file the residues colored by the Select Zone command? Best, Marco
The ChimeraX message when you run AlphaFold says:
"AlphaFold Prediction Requires Newer ChimeraX
Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or later.
The ChimeraX AlphaFold prediction service was broken by an update on Google Colab on March 14, 2024."
Is this unclear? You need to get a ChimeraX daily build newer than March 19, 2024. Those daily builds are on the ChimeraX download page.
Tom
On Apr 29, 2024, at 10:09 AM, Chang, Jufang via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Sir
Recently I can not use the ChimerX to do the alphafold prediction. The error message is some connection to the colab is broken sine March 2024. I am wondering when this feature of ChimeraX will come back?
Thank you
Ju-Fang
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu mailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thank you. The message is very clear. I didn’t pay enough attention that there is another version if I scrolled the screen down enough. I thought the first listed version on the download website is the latest version already.
取得 iOS 版 Outlookhttps://aka.ms/o0ukef ________________________________ 寄件者: Tom Goddard goddard@sonic.net 寄件日期: Wednesday, May 1, 2024 5:40:46 PM 收件者: Chang, Jufang jchang24@wustl.edu 副本: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu 主旨: Re: [chimerax-users] Alphafold
* External Email - Caution *
The ChimeraX message when you run AlphaFold says:
"AlphaFold Prediction Requires Newer ChimeraX
Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or later.
The ChimeraX AlphaFold prediction service was broken by an update on Google Colab on March 14, 2024."
Is this unclear? You need to get a ChimeraX daily build newer than March 19, 2024. Those daily builds are on the ChimeraX download page.
Tom
On Apr 29, 2024, at 10:09 AM, Chang, Jufang via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Sir
Recently I can not use the ChimerX to do the alphafold prediction. The error message is some connection to the colab is broken sine March 2024. I am wondering when this feature of ChimeraX will come back?
Thank you
Ju-Fang
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edumailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
participants (4)
-
Chang, Jufang -
Elaine Meng -
Marco Sette -
Tom Goddard