Re: [chimerax-announce] ChimeraX version 1.9 has been released
Hi Dietmar, Thanks for your comments. Unless you refer to data that must be kept private, it is best to send questions and suggestions to the chimerax-users mailing list (CC'd here) rather than to me or any other individual team member. That way the most relevent people can see/answer your question and other users can weigh in if they also wish for the same thing. You could use the Help menu to open the ChimeraX User Guide that is included with your download instead of googling the web. You can also use the context menu in each tool (or its Help button, if it has one), to open the ChimeraX manual page for that tool, and the "help" command to show the manual page for each ChimeraX command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/help.html> Unfortunately the ChimeraX Help menu does not have a search feature, although that is probably on our list of requests already. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 13, 2024, at 12:29 PM, Dietmar Funck <dietmar.funck@uni-konstanz.de> wrote:
Dear Elaine, dear ChimeraX developer Team,
thanks for the release of ChimeraX 1.9. I am confident that it will be as great or even better than 1.8 :-)
I have two requests/suggestions how your could improve ChimeraX further:
a) the metal coordination function seems to be still missing in ChimeraX (or it is so well hidden that I wasn’t able to find it).
b) You could teach Google that there is a difference between Chimera and ChimeraX. Each time, I try to find solutions to problems with ChimeraX, I get results from the user guide of Chimera, which usually don’t solve the problem.
All the best,
Dietma
Dietmar Funck Biopolymer Chemistry Chemistry Department University of Konstanz
Dear Elaine, thanks a lot for your immediate response and for forwarding my requests to the appropriate forum. Indeed, the ChimerX user guide did not help me to find a solution for the metal coordination problem. Perplexity couldn’t help either, but at least suggested I could use “ChimeraX” -Chimera in my google search. For the time being I might have to work alternatingly with either Chimera or ChimeraX, depending on which functions I prioritise at any given moment. Best wishes, Dietmar Dietmar Funck Biopolymer Chemistry Chemistry Department University of Konstanz Tel. +49 7531 884142
On 13. Dec 2024, at 21:38, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Dietmar, Thanks for your comments.
Unless you refer to data that must be kept private, it is best to send questions and suggestions to the chimerax-users mailing list (CC'd here) rather than to me or any other individual team member. That way the most relevent people can see/answer your question and other users can weigh in if they also wish for the same thing.
You could use the Help menu to open the ChimeraX User Guide that is included with your download instead of googling the web. You can also use the context menu in each tool (or its Help button, if it has one), to open the ChimeraX manual page for that tool, and the "help" command to show the manual page for each ChimeraX command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/help.html>
Unfortunately the ChimeraX Help menu does not have a search feature, although that is probably on our list of requests already.
Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 13, 2024, at 12:29 PM, Dietmar Funck <dietmar.funck@uni-konstanz.de> wrote:
Dear Elaine, dear ChimeraX developer Team,
thanks for the release of ChimeraX 1.9. I am confident that it will be as great or even better than 1.8 :-)
I have two requests/suggestions how your could improve ChimeraX further:
a) the metal coordination function seems to be still missing in ChimeraX (or it is so well hidden that I wasn’t able to find it).
b) You could teach Google that there is a difference between Chimera and ChimeraX. Each time, I try to find solutions to problems with ChimeraX, I get results from the user guide of Chimera, which usually don’t solve the problem.
All the best,
Dietma
Dietmar Funck Biopolymer Chemistry Chemistry Department University of Konstanz
Hi Dietmar, The Metal Geometry tool is one of a few things in Chimera that are still missing in ChimeraX that we would like to port. It could still be awhile since some other the other missing features (see UCSF ChimeraX vs. Chimera <https://www.rbvi.ucsf.edu/chimerax/progress.html>) are relatively high impact. Nonetheless we do want to get to Metal Geometry. I will open a feature-request ticket in our bug-tracking database with you cc’ed, so you will be kept informed about any progress on this front. In the interim, the SEQCROW bundle <https://cxtoolshed.rbvi.ucsf.edu/apps/seqcrow> has some metal-coordination capabilities that could be relevant (Swap Transition Metal Ligands; Coordination Complex Generator). --Eric Eric Pettersen UCSF Computer Graphics Lab
On Dec 13, 2024, at 12:47 PM, Dietmar Funck via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine,
thanks a lot for your immediate response and for forwarding my requests to the appropriate forum.
Indeed, the ChimerX user guide did not help me to find a solution for the metal coordination problem. Perplexity couldn’t help either, but at least suggested I could use “ChimeraX” -Chimera in my google search.
For the time being I might have to work alternatingly with either Chimera or ChimeraX, depending on which functions I prioritise at any given moment.
Best wishes, Dietmar
Dietmar Funck Biopolymer Chemistry Chemistry Department University of Konstanz
Tel. +49 7531 884142
On 13. Dec 2024, at 21:38, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Dietmar, Thanks for your comments.
Unless you refer to data that must be kept private, it is best to send questions and suggestions to the chimerax-users mailing list (CC'd here) rather than to me or any other individual team member. That way the most relevent people can see/answer your question and other users can weigh in if they also wish for the same thing.
You could use the Help menu to open the ChimeraX User Guide that is included with your download instead of googling the web. You can also use the context menu in each tool (or its Help button, if it has one), to open the ChimeraX manual page for that tool, and the "help" command to show the manual page for each ChimeraX command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/help.html>
Unfortunately the ChimeraX Help menu does not have a search feature, although that is probably on our list of requests already.
Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 13, 2024, at 12:29 PM, Dietmar Funck <dietmar.funck@uni-konstanz.de> wrote:
Dear Elaine, dear ChimeraX developer Team,
thanks for the release of ChimeraX 1.9. I am confident that it will be as great or even better than 1.8 :-)
I have two requests/suggestions how your could improve ChimeraX further:
a) the metal coordination function seems to be still missing in ChimeraX (or it is so well hidden that I wasn’t able to find it).
b) You could teach Google that there is a difference between Chimera and ChimeraX. Each time, I try to find solutions to problems with ChimeraX, I get results from the user guide of Chimera, which usually don’t solve the problem.
All the best,
Dietma
Dietmar Funck Biopolymer Chemistry Chemistry Department University of Konstanz
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participants (3)
-
Dietmar Funck -
Elaine Meng -
Eric Pettersen