- Chimera-users - RBVI Mailing Lists

Chimera running on a remote computer over ssh >>>> use virtualgl to avoid graphics problems
by Dieter Blaas 19 Sep '12

19 Sep '12

Those who encountered lots of problems with the graphics when running chimera remotely for example you receive error messages like this one: X Error of failed request: GLXBadContextTag Major opcode of failed request: 153 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1352 Current serial number in output stream: 1352 might be interested in the following solution: 1) install VirtualGL (http://www.virtualgl.org/) on both PCs 2) outcomment the indicated lines in the 'chimera' startup script 3) connect to the server by using 'vglconnect' 4) start chimera on the server with 'vglrun chimera' that's it! if [ -z "$nogui" ] then case "`uname -s`" in Linux) # preload our C++ runtime to avoid # ATI graphics driver bug # LD_PRELOAD=libotf.so <<<<<<<<< # export LD_PRELOAD <<<<<<<<< if test -e "$CHIMERA/bin/python2.7" then python="$CHIMERA/bin/python2.7" else in those cases where chimera works without this trick you might still see a substancial improvement in transmission speed! Best, Dieter -- ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Re: [Chimera-users] chimera utility help
by Elaine Meng 17 Sep '12

17 Sep '12

Dear Sotirios, You would use Join Models option "C-N peptide bond" as described in these instructions: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht…> "C-N peptide bond - specialized case of joining two peptides. The N-terminal N of one peptide and the C-terminal (carbonyl or carboxyl) C of the other should be selected. Each selected atom must be bonded to only one carbon; however, it may also be bonded to hydrogen and/or OXT, and if so, these atoms will be replaced as appropriate by the new peptide bond." If you do not see that option, maybe you have an older version of Chimera and should upgrade to a newer version. If you do see that option and you have followed the instructions as above but are still not able to apply, please save a session file and use menu "Help... Report a Bug" and attach the session file to the bugreport. I just tried it on two example proteins and seemed OK, but maybe there is something different about your structure. Thanks! Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 17, 2012, at 9:10 AM, Sotirios Katsamakas wrote: > Dear Elaine C. Meng, > I followed your suggestion and I created a separate side chain of the 25 amino acids with specified phi and psi values for its residues. But I am still not able to Join Models, through the homonymous section. I am selecting the C terminus of the constructed side chain (#0:25@C) and the N terminus of the protein (#1:26@N) respectively, but when I go to the panel the apply button stays inactive. I am sure it must be something obvious but it eludes me. Thank you in advance and I am looking forward in hearing from you. > > Best Regards, > Sotirios Katsamakas.

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Difference between atoms' coordinates on screen and in a PDB file
by Mateusz Dobrychłop 14 Sep '12

14 Sep '12

Hello, I load 3 protein models into Chimera and enter several "move" commands. The structures change their positions. Then, I save them as a PDB file, and immediately open the PDB file. The structures are not overlapping (screenshot: http://i.imgur.com/gtGBN.png ). Why does it work like this and what can I do to obtain accurate coordinates on my screen without re-opening the model (after I finish my sequence of translations)? Mateusz

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Denaturing a protein
by vamsee 14 Sep '12

14 Sep '12

Hi Elaine, Thanks for the answer for the previous question. I am back with one more :) Is there a way to completely denature a protein in Chimera? The idea is to completely unfold a particular protein (for ex: chemical denaturation GdHCl/Urea or thermal denaturation) to its primary structure. Also can this be modeled in such a way that we can extract thermodynamic parameters from the modeling? I do understand this sounds a lot like a Molecular Dynamics simulation but maybe there is a way in Chimera? Thanks again Vamsee

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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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H-bond analysis in case of TIP4P water model ?
by Marek Maly 04 Sep '12

04 Sep '12

Hello, it seem to me that Chimera is not able to do H-bond analysis between water molecules when TIP4P water model is used. Am I right or I overlooked something ? Thank you very much for the answer in advance ! Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Ligand parametrization
by Miro Moman 04 Sep '12

04 Sep '12

Hello, When energy minimising protein-ligand complexes, I have observed that Chimera seldom, if ever, complains about missing parameters. However, when I try to generate a Pmrtop file for the same complexes, quite often sLeap is unable to complete the request due to its inability to recognise certain atom types.. Provided that the minimization engine (MMTK) is using the Amber force filed, I was wondering: Are parameters computed in the same way? If not, what are the differences? Maybe a different forcefield version? In addition, is there a way to inspect the parameters that have been generated for minimising a given ligand or non-standard residue? Kind regards, Miro

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saving spheres
by MARY VARUGHESE 04 Sep '12

04 Sep '12

Hi, I saved the combined sph(two clusters) file. But the file contains two clusters with single ID, so i cant create the box including both clusters, since in the box.in file of dock i can give only one cluster number. How can i assign both clusters into single cluster. or any other suggestion. Thanking You.

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Fwd: Installation problems
by prashant kurkute 04 Sep '12

04 Sep '12

Respected sir, Sorry for making you disturb. I am novice to linux. I am trying to install chimera in ubuntu 12.04 LTS. I follow following instruction. sudo chmod +x chimera-1.6.2-linux_x86_64.bin ./chimera-1.6.2-linux_x86_64.bin (I also triied with root sudo ./chimera-1.6.2-linux_x86_64.bin) I got following reply bash: ./chimera-1.6.2-linux_x86_64.bin: cannot execute binary file Sir please help me to solve problem. I will be greatly thankful to your help. With Best wishes and regards.

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volume of an ensemble
by R. Andrew Byrd 31 Aug '12

31 Aug '12

Dear Chimera Team, Is it possible to get the total volume that encompasses an ensemble of structures? For example, if a docking or structure calculation produces an ensemble of structures, can one calculate the volume that encompasses all the members of the ensemble? A docking calculation may have one component superimposable and the second component represent an ensemble, and it is that ensemble that I would I like a measure of the total volume. Thanks! Andy

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adjust resolution of alignment .eps in Multalign viewer
by Gesa Volkers 30 Aug '12

30 Aug '12

Hi all, I would like to extract a high resolution publication quality image from my alignment from the Multalign viewer. Only option I see is to save it a as .eps, but when I open that file the resolution is not sufficient. Is it possible to get a higher resolution image? Thanks, Gesa

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reasonable minimization times
by David Belnap 30 Aug '12

30 Aug '12

I am trying to link the crystal structure of an Fc domain with two Fab structures. I am using the command "minimize spec sel fragment true" on the command line. When various options come up, I've selected "if alternate locations, keep only highest occupancy", "add hydrogens", "add charges", "consider each model in isolation from all others", "also consider H-bonds", and AMBER ff12SB and ANTECHAMBER to assign charges. I've had jobs run overnight that didn't finish. What is a reasonable time for about 8-10 residues to be minimized? Can you suggest any ways to speed this up? Thanks, David

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problem with loading color scheme in Multalign viewer
by Gesa Volkers 29 Aug '12

29 Aug '12

Hi all, I encountered a problem when I tried to open a color scheme (tried it with custom.par from the Chimera website) in the Multalign viewer. I get the following error: "File "C:\Program Files\Chimera 1.6.2\share\MultAlignViewer\PrefDialog.py", line 69, in addColorScheme self._resColorOpt.set(colorFile) See reply log for Python traceback." I reported a bug. Though has anyone found a way to solve this problem and is able to open a .par file again? Thanks, Gesa

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making a movie problem
by Boskovic.Jasminka 29 Aug '12

29 Aug '12

Hi, I am trying to make a movie with chimera but instead of filming just a molecule's movement the program is making the frames of all the chimera window showing the "File, Select, Actions etc" bottoms and the command line? How can I remove this option and film just the molecule window? Thank you in advance! Best regards, Jasminka Boskovic, PhD Centro Nacional de Investigaciones Oncologicas-CNIO (Spanish National Cancer Research Centre-CNIO) Melchor Fernandez Almagro 3 28029 Madrid Spain Tel.: + (34) 917 328 000 (ext 3031) Fax: + (34) 912 246 980 e-mail: jboskovic(a)cnio.es **NOTA DE CONFIDENCIALIDAD** Este correo electr�nico, y en su caso los ficheros adjuntos, pueden contener informaci�n protegida para el uso exclusivo de su destinatario. Se proh�be la distribuci�n, reproducci�n o cualquier otro tipo de transmisi�n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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Trivial question
by George Tzotzos 28 Aug '12

28 Aug '12

It seems that a standard feature of Chimera is upon loading a pdb file of a complex, a number of nearby residues also show up. My question is whether there's a rule, let's say a cutoff distance, or other. Thanks in advance for any advice on this Regards George

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Batch energy minimisation
by Miro Moman 24 Aug '12

24 Aug '12

Hello, Searching through the archives, I have found that performing DockPrep in batch mode is quite straightforward: http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html I have also noticed that, when working from the GUI, energy minimisation involves a previous DockPrep step. I would like to perform the energy minimisation of several protein-ligand complexes, can this be easily done in batch mode? Furthermore, I would also be interested of computing the binding energy both prior and after minimisation (possibly including APBS-computed electrostatic terms...). However, this is of secondary importance as it can be easily achieved with other tools. Best regards, Miro Moman

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