Hi Elaine I am using the contact tool from the structure analysis tool. It is giving me a few pseudobonds and I want to delete a few of them for the picture I am working on. I also tried checking the pseudobond command. So, could you please help me in specifying pseudo bonds and how to delete or hide specified pseudobonds in the figure, instead of all of them. Thanks a lot !! Regards Ruchika
Hi Ruchika, If you want to hide only some specific contacts pseudobonds, there are several ways. (A) One way is to select them (Ctrl-click, Shift-Ctrl-click on them in the graphics window so that they have a green outline) and then use command hide sel pseudobonds (B) Another way is to hide the atom on at least one end of the pseudobond, which will also automatically hide the pseudobond. (C) Another approach is to use the Contacts options to limit the calculation to only selected atoms so you don't get the extra ones you didn't want in the first place. See the "Limit by selection" options: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 15, 2021, at 4:10 AM, Ruchika Bajaj <phd.ruchika@gmail.com> wrote:
Hi Elaine
I am using the contact tool from the structure analysis tool. It is giving me a few pseudobonds and I want to delete a few of them for the picture I am working on. I also tried checking the pseudobond command. So, could you please help me in specifying pseudo bonds and how to delete or hide specified pseudobonds in the figure, instead of all of them.
Thanks a lot !! Regards Ruchika
Hi Elaine On Thu, Apr 15, 2021 at 8:57 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ruchika, If you want to hide only some specific contacts pseudobonds, there are several ways.
(A) One way is to select them (Ctrl-click, Shift-Ctrl-click on them in the graphics window so that they have a green outline) and then use command
hide sel pseudobonds
I tried to use this option, however, it works sometimes, but not other times. Can you please explain to me a bit more ?
(B) Another way is to hide the atom on at least one end of the pseudobond, which will also automatically hide the pseudobond.
It didn't work with me either.
(C) Another approach is to use the Contacts options to limit the calculation to only selected atoms so you don't get the extra ones you didn't want in the first place. See the "Limit by selection" options: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html>
I tried this one, but it didn't help completely.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 15, 2021, at 4:10 AM, Ruchika Bajaj <phd.ruchika@gmail.com> wrote:
Hi Elaine
I am using the contact tool from the structure analysis tool. It is giving me a few pseudobonds and I want to delete a few of them for the picture I am working on. I also tried checking the pseudobond command. So, could you please help me in specifying pseudo bonds and how to delete or hide specified pseudobonds in the figure, instead of all of them.
Thanks a lot !! Regards Ruchika
Hi Ruchika, It is not possible to answer unless you give more details about what you mean when you say it doesn't work or didn't help completely... like every detailed step of what you tried and what happened at each step. Maybe you did something wrong or maybe there is a bug. Also you could attach a specific session file and say exactly which pseudobond(s) you are unable to hide in that session. Elaine
On Apr 17, 2021, at 6:09 AM, Ruchika Bajaj <phd.ruchika@gmail.com> wrote:
Hi Elaine On Thu, Apr 15, 2021 at 8:57 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ruchika, If you want to hide only some specific contacts pseudobonds, there are several ways.
(A) One way is to select them (Ctrl-click, Shift-Ctrl-click on them in the graphics window so that they have a green outline) and then use command
hide sel pseudobonds
I tried to use this option, however, it works sometimes, but not other times. Can you please explain to me a bit more ?
(B) Another way is to hide the atom on at least one end of the pseudobond, which will also automatically hide the pseudobond.
It didn't work with me either.
(C) Another approach is to use the Contacts options to limit the calculation to only selected atoms so you don't get the extra ones you didn't want in the first place. See the "Limit by selection" options: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html>
I tried this one, but it didn't help completely.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 15, 2021, at 4:10 AM, Ruchika Bajaj <phd.ruchika@gmail.com> wrote:
Hi Elaine
I am using the contact tool from the structure analysis tool. It is giving me a few pseudobonds and I want to delete a few of them for the picture I am working on. I also tried checking the pseudobond command. So, could you please help me in specifying pseudo bonds and how to delete or hide specified pseudobonds in the figure, instead of all of them.
Thanks a lot !! Regards Ruchika
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