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