Manipulating representation during MD movie
Hi guys, I have a MD movie I generated that I want to record. However, I would need to ask on the graphical representation at given frames (i.e. frame 60) so that the system changes (i.e. change the representation en stick or add a given label). Is there a way to do so directedly? Or should I go for a command file? In this case, how would I mix the MD movie with my own succession of events? All the best, JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-users-request@cgl.ucsf.edu Data: Dilluns, Febrer 6, 2012 9:00 pm Assumpte: Chimera-users Digest, Vol 106, Issue 7
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Today's Topics:
1. Rotamer copying (Ahir Pushpanath) 2. Re: Rotamer copying (Eric Pettersen)
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Message: 1 Date: Mon, 6 Feb 2012 18:51:22 +0000 From: Ahir Pushpanath <ahir29@googlemail.com> To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] Rotamer copying Message-ID: <CAMVKkxyEoXbnQUo7hxa+m2-u5wLCvMJn7DDY=hzZPJEbC_OvSw@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1"
Hello there, I have a question regarding MODELLER in Chimera and the ability of chimera to adjust the model using some inbuilt features quickly(i.e. automatically, instead of interactively)
Firstly, I am trying to model the "holo" form of an enzyme with known apo-form structure. I did this usinig the two independent domains of the apo form as a template (in a bid to get the domains accurate) and for the holo-form closure I used a very similar homologue that has been solved in the holo form. The results were good and I got a decent model that had closed up like the homolog.
However, I noticed that in the model a lot of the sidechains have not been modelled with the right rotamer. This is odd, as I gave it the two independent domains as a template, so it had all the information it neededto get that perfectly right.
Either way, this means, I need to manually "copy" the rotamers from the apo form onto the "holo model", which is time consuming. I know from the homolog that only two or three residues in the active site change rotamerupon apo-holo conformational change. So, I just want an easy way to edit the rotamers in the holo-model to copy the rotamers of the apo-form for all residues.
Is there an easy way to do this, is it possible to this with a script? I have no idea how to script, mind you!
Ahir
Hi JD, Two general possibilities: (A) mostly graphical interface: you could use "Per-Frame... Define script" in the MD Movie dialog. There is a way to indicate commands should execute at specific frames. There is an example in the manual page, see the "Per-frame scripts" section: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> You could try playback without recording just to make sure it really does what you want, and then use "File... Record movie" in the MD Movie dialog to set up and do the recording. For details, see the "Recording a movie" section in the manual page. (B) do everything with a script: if Chimera command script, you can use the command "coordset" to play specific frames or frame ranges of your trajectory, and in between those, you can put your other commands. For example, you could play frames 1-10, then color something, then play frames 11-20, etc. You would also have to use the "movie" command to start and stop recording and encode to movie file. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html> There are some example Chimera command scripts, the "trmovie" one includes using "coordset": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 7, 2012, at 5:49 AM, Jean Didier Pie Marechal wrote:
Hi guys,
I have a MD movie I generated that I want to record. However, I would need to ask on the graphical representation at given frames (i.e. frame 60) so that the system changes (i.e. change the representation en stick or add a given label). Is there a way to do so directedly? Or should I go for a command file? In this case, how would I mix the MD movie with my own succession of events?
All the best, JD
participants (2)
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Elaine Meng -
Jean Didier Pie Marechal