February 2012 - Chimera-users - RBVI Mailing Lists

minimization with nonstandard atoms
by Jon N. Rumbley 07 Feb '12

07 Feb '12

I was hoping to minimize a homology model containing two heme groups. To understand how I might do this I have been starting with the known structure 1a6m. As suggested in the documentation I begin with Dock Prep and calculate charges etc. To my surprise Chimera alpha version 1.6 (build 34702) actually assigned charges to the heme. The problem is with the minimization itself. Within Minimize Structure I turn off all of the Dock Prep steps and simply try to minimize the structure but get an error,"Element Fe (atom #0:154.A@FE) is not currently supported". I was assuming the charge calc was going to be the hard part but now I am stuck at this subsequent step. Is there something I can do to get the heme atoms recognized or is this simply not possible? Thank you, Jon Rumbley Dr. Jon N. Rumbley Assistant Professor Dept. of Pharmacy Practice and Pharmaceutical Sciences University of Minnesota-Duluth 127 Life Sciences 1110 Kirby Dr. Duluth, MN 55812 Phone: 218-726-6047 email: jrumbley(a)d.umn.edu

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Manipulating representation during MD movie
by Jean Didier Pie Marechal 07 Feb '12

07 Feb '12

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(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-users-request(a)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(a)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(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)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(a)googlemail.com> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] Rotamer copying > Message-ID: > <CAMVKkxyEoXbnQUo7hxa+m2-u5wLCvMJn7DDY=hzZPJEbC_OvSw(a)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 >

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how to find salt bridge
by Bishwajit Das 04 Feb '12

04 Feb '12

how to find salt bridge in a docked structure........plz help me -- * BISHWAJIT DAS* *+91-9433237920* KOLKATA

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Coloring electrostatic potential
by George Tzotzos 03 Feb '12

03 Feb '12

Hi everybody, I'm using SiteHound for ligand binding identification sites. I'm comparing the highest affinity sites for two superimposable receptors. I'm attaching an example where the sites favourable to protein 1 are shown red, whereas those for protein two blue. I've opened in Chimera the file that contains the red and blue clusters (difference.pdb) as well as the corresponding potential file (potential.dx). I used the Volume Viewer to different affinity areas but had .... no luck. Any help would be greatly appreciated Best regards George

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export saved session
by Gabor PAPAI 02 Feb '12

02 Feb '12

Dear Chimera team, Is it possible to export a session with all of its files to a different location - for e.g. to a USB flash drive for portability reason? I'd like to open a session saved to a server on an offline computer (during travel). I know that I can do it manually just I'm searching for quick solution. Thank you in advance for the help! Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-88655748

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selection based on ring names
by Bala subramanian 02 Feb '12

02 Feb '12

Friends, I have two ligands with a common benzoxadiazole ring. I want to do the rmsd comparison only on the ring, but the names of the atoms forming the benzoxadiazole ring are different in both the ligands. Is there any way to use ring name as a string the compare the rmsd. ie. rmsd of benzoxadiazole of ligand 1 and benzoxadiazole ring of ligand 2 -- C. Balasubramanian

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stereo with zalman monitor
by Jose Miguel Mancheno 01 Feb '12

01 Feb '12

Dear colleagues, I am trying to see stereo images with chimera (candidate version 1.6 for mac) using a Zalman monitor ZM240W which works OK with COOT, which is connected to an iMac. As far as I know, I have to select (within the camera mode) the option: row stereo, right eye even (or odd). However, none of these options provided stereo images. If I select sequential stereo (or reverse sequential stereo) I see the image flickering, as expected, but this is not synchronized with the zalman glasses. Any suggestion about how to proceed to see in stereo mode? Thank you very much in advance. José Miguel --

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Selecting equivalent surfaces
by Ankush Aggarwal 01 Feb '12

01 Feb '12

Hi, I am opening up a viperDB file of a T=3 virus in Chimera. I want to select the 60 equivalent copies of a protein, so that I can change their color together. I am able to select selecting each of them separately. Is there a smarter way to do it? Also, after I rotate the view, is there a command to reset it to the default. Right now, I am "undoing" the move, but it can be a pain if I have moved the model a few times. Thanks, Ankush.

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Notebook
by Miguel Ortiz Lombardía 01 Feb '12

01 Feb '12

Dear all, Was the notebook feature implemented in Chimera? I found a message from some time ago but nothing else? Any plans to include a session notebook? I would ask for something really simple, just apt for text notes. Currently, I create text files with the same name than sessions but with .txt extension, however I think it would be useful to have this built-in in Chimera. Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

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Chimera-users February 2012