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.
Dear all, May I save in a file the residues colored by the Select Zone command? Best, Marco -- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail:sette@uniroma2.it e-mail:m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette
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 Outlook<https://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.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/ ________________________________ 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)
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Chang, Jufang -
Elaine Meng -
Marco Sette -
Tom Goddard