Dear ChimeraX Developers, I apologize for disturbing you, I have a question, how can I make pseudobonds in ChimeraX similar to Chimera? I mean when I try to create hydrogen bonds, by default, in Chimera (Tools->structure analysis->findHbonds) they appear as lines (or sticks), connected to the structure (left image). But if I export the model and import it in ChimeraX bonds become "disconnected". The same appeared if I place H-bonds directly in ChimeraX (right image). If I select pesudobond, an option of changing its length manually is unavailable. The structure is attached if needed. [cid:image002.png@01D9C590.A8D2F3A0] Thank you in advance! Best regards, Aleksei
Hi Aleksei, We think you may need to get a newer version of ChimeraX -- testing in a ChimeraX daily build from 7/31, we did not see gaps between pseudobonds and ribbons with either of these: (1) calculating H-bonds in Chimera, exporting to ChimeraX, opening exported file in ChimeraX (2) opening your structure and calculating hbonds in ChimeraX, see image attached below including Log with the commands that were used However, we do see the gaps in the 1.6.1 release from May, which we found somewhat surprising because we thought it was fixed before then. But regardless, you can get the current 1.7 daily build from the download page: <https://www.rbvi.ucsf.edu/chimerax/download.html> Unfortunately the daily build gives a traceback opening the export from Chimera, but we believe that is just in setting the window size at the end, whereas the contents are present, so it should be OK to proceed after you resize the window as you like. Some other problems with the export/import are that the Chimera pseudobonds are cyan and solid, whereas in ChimeraX they show up as dashed yellow. We have noted all these problems and will work on fixing them. You can also change the color and style of the pseudobonds in ChimeraX after import with commands "color" and "style" However: You might as well skip the export/import and just do everything in ChimeraX instead: the hydrogen-bonding calculation is the same and both the hbonds command and the H-Bonds tool have been improved to make them easier to use compared to Chimera. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/hbonds.html> The Log in the screenshot below shows using the hbonds command, which (details in help, link above) includes options for pseudobond color, style, and radius (stick thickness). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 2, 2023, at 12:28 PM, Aleksei Solomonov via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Developers,
I apologize for disturbing you, I have a question, how can I make pseudobonds in ChimeraX similar to Chimera? I mean when I try to create hydrogen bonds, by default, in Chimera (Tools->structure analysis->findHbonds) they appear as lines (or sticks), connected to the structure (left image). But if I export the model and import it in ChimeraX bonds become “disconnected”. The same appeared if I place H-bonds directly in ChimeraX (right image). If I select pesudobond, an option of changing its length manually is unavailable. The structure is attached if needed. <image002.png>
Thank you in advance!
Best regards, Aleksei <30.pdb>
Thanks a lot! I will try! I also have a question, is it possible to make a donation to ChimeraX project? Best, Alex From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 2 August 2023 23:53 To: Aleksei Solomonov <aleksei.solomonov@weizmann.ac.il> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Pseudobonds question Hi Aleksei, We think you may need to get a newer version of ChimeraX -- testing in a ChimeraX daily build from 7/31, we did not see gaps between pseudobonds and ribbons with either of these: (1) calculating H-bonds in Chimera, exporting to ChimeraX, opening exported file in ChimeraX (2) opening your structure and calculating hbonds in ChimeraX, see image attached below including Log with the commands that were used However, we do see the gaps in the 1.6.1 release from May, which we found somewhat surprising because we thought it was fixed before then. But regardless, you can get the current 1.7 daily build from the download page: <https://www.rbvi.ucsf.edu/chimerax/download.html> Unfortunately the daily build gives a traceback opening the export from Chimera, but we believe that is just in setting the window size at the end, whereas the contents are present, so it should be OK to proceed after you resize the window as you like. Some other problems with the export/import are that the Chimera pseudobonds are cyan and solid, whereas in ChimeraX they show up as dashed yellow. We have noted all these problems and will work on fixing them. You can also change the color and style of the pseudobonds in ChimeraX after import with commands "color" and "style" However: You might as well skip the export/import and just do everything in ChimeraX instead: the hydrogen-bonding calculation is the same and both the hbonds command and the H-Bonds tool have been improved to make them easier to use compared to Chimera. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/hbonds.html> The Log in the screenshot below shows using the hbonds command, which (details in help, link above) includes options for pseudobond color, style, and radius (stick thickness). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco [cid:image001.png@01D9C59D.15A236B0] On Aug 2, 2023, at 12:28 PM, Aleksei Solomonov via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear ChimeraX Developers, I apologize for disturbing you, I have a question, how can I make pseudobonds in ChimeraX similar to Chimera? I mean when I try to create hydrogen bonds, by default, in Chimera (Tools->structure analysis->findHbonds) they appear as lines (or sticks), connected to the structure (left image). But if I export the model and import it in ChimeraX bonds become “disconnected”. The same appeared if I place H-bonds directly in ChimeraX (right image). If I select pesudobond, an option of changing its length manually is unavailable. The structure is attached if needed. <image002.png> Thank you in advance! Best regards, Aleksei <30.pdb>
participants (2)
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Aleksei Solomonov -
Elaine Meng