[Chimera-users] Manipulating representation during MD movie
Jean Didier Pie Marechal
JeanDidier.Marechal at uab.cat
Tue Feb 7 05:49:26 PST 2012
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 at uab.es
www: http://asklipio.qf.uab.es
----- Missatge original -----
De: chimera-users-request at cgl.ucsf.edu
Data: Dilluns, Febrer 6, 2012 9:00 pm
Assumpte: Chimera-users Digest, Vol 106, Issue 7
> Send Chimera-users mailing list submissions to
> chimera-users at cgl.ucsf.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> or, via email, send a message with subject or body 'help' to
> chimera-users-request at cgl.ucsf.edu
>
> You can reach the person managing the list at
> chimera-users-owner at cgl.ucsf.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Chimera-users digest..."
>
>
> Today's Topics:
>
> 1. Rotamer copying (Ahir Pushpanath)
> 2. Re: Rotamer copying (Eric Pettersen)
>
>
> --------------------------------------------------------------------
> --
>
> Message: 1
> Date: Mon, 6 Feb 2012 18:51:22 +0000
> From: Ahir Pushpanath <ahir29 at googlemail.com>
> To: chimera-users at cgl.ucsf.edu
> Subject: [Chimera-users] Rotamer copying
> Message-ID:
> <CAMVKkxyEoXbnQUo7hxa+m2-u5wLCvMJn7DDY=hzZPJEbC_OvSw at 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
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-
> users/attachments/20120206/098eb318/attachment-0001.html>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 6 Feb 2012 11:55:54 -0800
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> To: Ahir Pushpanath <ahir29 at googlemail.com>
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Rotamer copying
> Message-ID: <1E6304DE-DE11-49BF-A0CA-3538CE763E8D at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"; Format="flowed";
> DelSp="yes"
>
> I have attached a script that, if you have exactly two models open
> and
> they have the same residues, will copy the chi angles of the lower-
> numbered model into the higher-numbered model. You can run the
> script
> simply by opening it with File->Open.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
>
>
>
> On Feb 6, 2012, at 10:51 AM, Ahir Pushpanath wrote:
>
> > 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 needed to 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 rotamer upon 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
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-
> users/attachments/20120206/62334b47/attachment-0002.html>
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: copyChis.py
> Type: text/x-python-script
> Size: 431 bytes
> Desc: not available
> URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-
> users/attachments/20120206/62334b47/attachment-0001.bin>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-
> users/attachments/20120206/62334b47/attachment-0003.html>
>
> ------------------------------
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
> End of Chimera-users Digest, Vol 106, Issue 7
> *********************************************
>
More information about the Chimera-users
mailing list