calculating radius of gyration
On Dec 14, 2021, at 11:10 AM, Simon.Chapman <simon.chapman@open.ac.uk> wrote:
Hello again Elaine. All going very well with Chimera, and I've introduced the software to some more of mt students.
But, is there a way to plot radius of gyration from the simualtion data? I would have thought somehow the RMSD over time should allow that?
Best wishes
Hi Simon, Thanks for introducing others to Chimera! I'm not the expert on this topic, so I had to consult with others to answer this question. Just as a reminder, it's recommended to send questions to chimera-users@cgl.ucsf.edu (CC'd here) unless what you are sending needs to remain private. I don't know everything (surprise!) or I might not understand your question as well as somebody else does. RMSD compares different sets of coordinates, so I don't think that gets you anything like the radius of gyration of a single set of coordinates. There are some scripts to calculate radius of gyration on the Chimera Python Scripts page: <https://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
Thank you for the prompt reply Elaine. I hadn't spotted this link even though I had rummaged through Chimera help. The scripts look very useful. But I'm not sure where they woud be run..these don't look like Chimera command line instructions? The first line seems very unfamiliar...perhaps "Pett" might elucidate? Or one of your colleagues if you are also uncertain about their use? Best wishes Simon ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 14 December 2021 20:29 To: Simon.Chapman <simon.chapman@open.ac.uk> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: calculating radius of gyration CAUTION: This mail comes from outside the University. Please consider this before opening attachments, clicking links, or acting on the content.
On Dec 14, 2021, at 11:10 AM, Simon.Chapman <simon.chapman@open.ac.uk> wrote:
Hello again Elaine. All going very well with Chimera, and I've introduced the software to some more of mt students.
But, is there a way to plot radius of gyration from the simualtion data? I would have thought somehow the RMSD over time should allow that?
Best wishes
Hi Simon, Thanks for introducing others to Chimera! I'm not the expert on this topic, so I had to consult with others to answer this question. Just as a reminder, it's recommended to send questions to chimera-users@cgl.ucsf.edu (CC'd here) unless what you are sending needs to remain private. I don't know everything (surprise!) or I might not understand your question as well as somebody else does. RMSD compares different sets of coordinates, so I don't think that gets you anything like the radius of gyration of a single set of coordinates. There are some scripts to calculate radius of gyration on the Chimera Python Scripts page: <https://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
Hi Simon, After poking around the chimera-users archive after googling it for "radius of gyration" I recommend looking at these previous posts (and possibly others in their threads, but these seem to be the most important): <https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008736.html> <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-April/013318.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. you can google the archive from this page <https://www.rbvi.ucsf.edu/chimera/docs/feedback.html>
On Dec 14, 2021, at 1:45 PM, Simon.Chapman via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thank you for the prompt reply Elaine. I hadn't spotted this link even though I had rummaged through Chimera help.
The scripts look very useful. But I'm not sure where they woud be run..these don't look like Chimera command line instructions? The first line seems very unfamiliar...perhaps "Pett" might elucidate? Or one of your colleagues if you are also uncertain about their use?
Best wishes
Simon
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 14 December 2021 20:29 To: Simon.Chapman <simon.chapman@open.ac.uk> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: calculating radius of gyration
CAUTION: This mail comes from outside the University. Please consider this before opening attachments, clicking links, or acting on the content.
On Dec 14, 2021, at 11:10 AM, Simon.Chapman <simon.chapman@open.ac.uk> wrote:
Hello again Elaine. All going very well with Chimera, and I've introduced the software to some more of mt students.
But, is there a way to plot radius of gyration from the simualtion data? I would have thought somehow the RMSD over time should allow that?
Best wishes
Hi Simon, Thanks for introducing others to Chimera!
I'm not the expert on this topic, so I had to consult with others to answer this question. Just as a reminder, it's recommended to send questions to chimera-users@cgl.ucsf.edu (CC'd here) unless what you are sending needs to remain private. I don't know everything (surprise!) or I might not understand your question as well as somebody else does.
RMSD compares different sets of coordinates, so I don't think that gets you anything like the radius of gyration of a single set of coordinates.
There are some scripts to calculate radius of gyration on the Chimera Python Scripts page: <https://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Elaine Meng -
Simon.Chapman