- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Rotamer copying- Specific Residues only
by Eric Pettersen 08 Feb '12

08 Feb '12

On Feb 8, 2012, at 8:27 AM, Ahir Pushpanath wrote: > Eric, although the script is highly useful for what I previously > asked, I have come to the realisation that simply copying all the > apo chi angles to the holo form may not be ideal for me in this > particular situation. I noted that of around 200 residues modelled, > around 90 of them are modelled different to the apo, the rest are > modelled similar to the apo form. Of these 90, only around half are > truly changed in the holo form(literature evidence from homolog), > therefore I do require a script that is able to accept an input of > which residues to copy the chi angles for, I think this will be > useful for other users who want to copy chi angles from apo-holo > forms and other applications, and probably could be included in > later build versions of chimera, under structure editing. > > Do you think you could help me with this? I am only learning python > now, so my scripting is not at a good level for these types of things. I've attached a modified script that will only copy the chi angles for residues that are selected in the lowered-numbered model. It's up to you to select them somehow. :-) > On another note, do you have any experience with using chimera to > model apo-holo transitions any other way without using Modeller? I don't. Maybe others on the list will have suggestions... ? > Also, does chimera have the ability to do docking of ligands, i.e. > given you know the apo crystal structure, can you tell it to dock a > ligand and change conformation of protein,(similar to autodock)? Currently Chimera cannot dock ligands. If our next 5 years of funding gets approved by the NIH, we have proposed interfacing Chimera to an Autodock Vina web service that would allow docking to be carried out directly from Chimera. Right now all you can do is prepare the input for / analyze the output of external docking programs in Chimera --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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how to find hydrophobic interaction
by Bishwajit Das 08 Feb '12

08 Feb '12

how to find hydrophobic interaction in a docked protein structure......please help me.... -- BISHWAJIT DAS +91-9433237920 KOLKATA,West Bengal INDIA* *

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how to setup a default settings for a new pdb model?
by Xing Zhang 07 Feb '12

07 Feb '12

Hi, I have many different pdb models that need to be displayed at exactly the same settings, including color, background, stick scale and so on, so I want to set all these settings for the first model, and then apply these settings to a newly opened pdb model. Is there any way to save and load a default setting for a new pdb model? Thanks much. Xing

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Rotamer copying
by Ahir Pushpanath 07 Feb '12

07 Feb '12

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

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associating multiple structures and sequences
by Uppal, Karan 07 Feb '12

07 Feb '12

Hi, I am writing a custom extension based on MultiAlign Viewer that highlights regions in a multiple sequence alignment based on numerical values stored in an external file. I modified the RegionBrowser.py script, and added a function that works just like "showSS". It works fine for one structure and sequence combination. However, I am trying to associate multiple copies of the same protein structure and its sequence. So, the structures are identical and so are the sequences in the sequence alignment, but each copy represents different information. My problem is that the sequences in the alignment viewer dialog box are highlighted in a random fashion. And, I want the sequences to be highlighted in an ordered fashion starting from first sequence to last sequence since we want to be able to map the highlighted regions back to the external file. Is there a way to control the order in which the sequences are highlighted in the alignment viewer dialog? Or is there a way to get the model # associated with a particular sequence and using the model # to highlight the alignment viewer? I would highly appreciate your help. Thank you, Karan Uppal Application Developer Emory University ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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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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