- Chimera-users - RBVI Mailing Lists

sphgen format
by Brian Fochtman 13 Sep '12

13 Sep '12

Hello, I read in the release notes for version 1.6 that Chimera is now able to input files in the dock .sph format. Thank you for this feature, it will be very helpful. Unfortunately I am having some trouble using it. (File -> Open -> file.sph) declares a syntax error for the following file (I've only included the beginning of the file because the output says the synax error is on line 2). Is there another method to read in these files? Thank you, Brian Fochtman cluster 1 number of spheres in cluster 72 1 20.51900 -17.55400 15.86300 0.700 1 2 21.04300 -18.55700 16.07400 0.700 2 3 22.17700 -17.60500 16.24100 0.700 3 4 22.17500 -17.84200 15.30900 0.700 4 5 21.41300 -20.08800 15.15700 0.700 5 6 20.64000 -20.83100 16.58800 0.700 6 7 21.63200 -18.65500 14.15300 0.700 7 8 23.13800 -16.98900 16.54500 0.700 8 9 21.18800 -21.21200 14.71200 0.700 9 10 17.88800 -26.45300 19.89900 0.700 10 11 21.83900 -17.33000 12.81300 0.700 11 12 21.28600 -20.42100 13.28900 0.700 12 13 23.77100 -15.65400 16.91100 0.700 13 14 21.15100 -21.76500 13.92000 0.700 14 15 21.38500 -19.46300 12.20200 0.700 15 16 20.39500 -21.75600 13.41100 0.700 16

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Gromac .xtc format
by Eric Pettersen 13 Sep '12

13 Sep '12

Hi, For you Chimera/Gromacs users out there, the current daily build allows you to use .xtc format coordinates now as an alternative to .trr . --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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chimera utility help
by Sotirios Katsamakas 13 Sep '12

13 Sep '12

Dear sir or madam, I am a recent user of the chimera software on Linux-Ubuntu (11.10) operating system and I confronted a dead end on the following issue. I reconstructed a missing side chain of 25 amino acids in a PDB file but I cant seem to find how to set the secondary structure and so on for these 25 residues. So they are stuck in a linear formation externaly from my protein. For your consideration I am attaching also the PDB file. Thank you in advance and looking forward in hearing from you regarding my problem. Best Regards, Sotirios Katsamakas

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Re: [Chimera-users] Match->Align command line option?
by Eric Pettersen 12 Sep '12

12 Sep '12

On Sep 12, 2012, at 11:16 AM, Chetanya Pandya wrote: > Hello, > > I want to superimpose multiple structure sets and get the corresponding multiple sequence alignments using Chimera. I've been using the Match->Align option from the Tools menu. Now, I want to automate the process using the Python interface. > > Unfortunately, I'm unable to find a command line option which does this. Can you help me out with this? Hi Chetanya, It's a little ambiguous if you are asking about a command version of Match->Align, or how to call it from Python. The issue is moot though since there currently is no command version of Match->Align, so you have to call it from Python! I don't know how familiar you are with Python or programming with Python, but the Chimera Programmer's Guide has some info to help. http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html If you don't know Python at all, follow the link in the Guide to the Python Tutorial and work through that, or at least the first few sections of that. Then for some Chimera-specific info, look at some of the Examples and the "basic primer" linked on the page. Assuming you've written a script that has gotten to the stage where the structures are already open and superimposed, here's the info you'll need to use the Match->Align API: 1) Getting the list of open molecules: from chimera import openModels, Molecule mols = openModels.list(modelTypes=[Molecule]) 2) Getting the list of chains to use. This example code assumes they're chain A: chains = [m.sequence('A') for m in mols] 3) Call Match->Align to create the alignment. from StructSeqAlign import makeAlignment mav = makeAlignment(chains) Note that the makeAlignment call will only return the Multalign Viewer instance starting with tomorrow's daily build (i.e. I made that change today!). Also, the makeAlignment call has a lot of optional arguments to change the parameters used in computing the alignment (e.g. cutoff, iteration, reference chain). Look at <your Chimera>/share/StructSeqAlign/__init__.py to see what the options are if you need to change the default behavior. (On a Mac, "<your Chimera>" is Chimera.app/Contents/Resources). 4) Save the alignment to a FASTA format file (named "x.fa") and Quit the MAV instance: f = open("x.fa", "w") from MultAlignViewer.formatters.saveFASTA import save save(f, mav, mav.seqs, mav.fileMarkups) f.close() mav.Quit() I hope this helps. Since this is pretty Python-intensive, I set followups to go to the chimera-dev mailing list rather than chimera-users. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Visualization of protein aqueous solution
by Nikolay Igorovich Rodionov 10 Sep '12

10 Sep '12

Hi all, Could anyone tell me how I could solvate my protein in a solution of a specific molarity solution with both water molecules and Na+ Cl- ions. I have no trouble adding the water molecules, but I am not sure how to go about adding the ions into the visualization. I've tried using add-ion but I haven't had good results. Are there any other options? This is for purely visual purposes, I'm creating a conceptual image, so I don't need the system to be 100% accurate or capable of conducting calculations. Much Thanks! Nikolay Rodionov

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color by RMSD
by Daniel Gurnon 10 Sep '12

10 Sep '12

Hi everyone, To color a trajectory by RMSD, comparing each frame to the final frame. My approach was to save the last frame of the trajectory as a pdb, load it as a separate model, and then run something like this script: mm #0 #1 show true rangecolor mavRMSD min white mid pink max red This works, but of course my screen quickly fills with multialign-viewer windows. Without "show true" in the script, coloring doesn't work past the first frame. Is there a way to do this without displaying the MAV window? thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Ribbon gradient coloring
by vamsee 10 Sep '12

10 Sep '12

Hi All, Is there a way to color the ribbon with a gradient? In my case, it has to be an increasing and then decreasing gradient. Ex: Let's say I have data that shows that a certain region of a protein is highly dynamic. This region consists of approx 11 residues and the most dynamic region in these 11 are the residues 5,6 and 7. Now, I need to color the ribbon in such a way that residues 1 and 11 are the same color (green), 2 and 10 (yellow), 3 and 9 (light orange) 4 and 8 (orange) 5,6 and 7 (red). I could do this by coding it but it becomes a step gradient and it doesn't look so good plus if I need to do this for residues in a bunch of proteins/peptides, the task quickly becomes tedious. I would rather write 2 lines of code for the complete protein than write 1 line/residue/protein. Any ideas? Thanks in advance Vamsee

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selection of multiple atoms in a session with multiple pdb structures
by Anindito Sen 09 Sep '12

09 Sep '12

Dear All, I have a Chimera session where 4 different atomic structures (pdb files) are docked in the computed density map of a macromolecular complex. I need to select multiple amino acids positioned at different places of the different docked atomic structures. To explain the situation- Say the 4 docked Atomic structures are A, B, C & D I need to select 276aa of A, 15aa of B, 246aa of C and so on... How can I do that ? Thanks Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

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Distance between two benzene rings
by George Tzotzos 06 Sep '12

06 Sep '12

Hi everybody, I'm trying to work out stacking interactions between two benzene rings. Is there a way to measure the distance from the center of the benzene rings of a Tyr to the center of the benzene ring of a Phe residue? Your help suggestions / help much appreciated as always Regards George

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Fwd: [Chimera] #11323: Chimera using local GLUT installation (was: Chimera bug report submission)
by George Tzotzos 05 Sep '12

05 Sep '12

Apologies for sending this to the List but I haven't received any information regarding the bug report below. Maybe I missed the mail. I have reinstalled Chimera but I get the same error message. Any suggestions how to solve this problem? Many thanks George Begin forwarded message: > From: Chimera <chimera-bugs-admin(a)cgl.ucsf.edu> > Subject: Re: [Chimera] #11323: Chimera using local GLUT installation (was: Chimera bug report submission) > Date: August 27, 2012 7:12:02 PM GMT+02:00 > To: Undisclosed recipients: ; > Reply-To: chimera-bugs(a)cgl.ucsf.edu > > #11323: Chimera using local GLUT installation > ---------------------------------+------------------------------------- > Reporter: gtzotzos@… | Owner: gregc > Type: defect | Status: assigned > Priority: normal | Milestone: Release 1.7 > Component: Platform | Version: 1.6.2 (b36855) > Severity: normal | Resolution: > Keywords: | Blocked By: > Blocking: | Notify when closed: > Platform: Mac OS X (Cocoa 64) | Project: chimera > ---------------------------------+------------------------------------- > Changes (by pett): > > * status: new => assigned > * component: Unassigned => Platform > * project: => chimera > * platform: => Mac OS X (Cocoa 64) > * version: => 1.6.2 (b36855) > * milestone: => Release 1.7 > * owner: pett => gregc > > > -- > Ticket URL: <http://plato.cgl.ucsf.edu/trac/chimera/ticket/11323#comment:1> > Chimera <http://plato.cgl.ucsf.edu/trac/chimera> > Chimera Issue Tracker

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