- Chimera-users - RBVI Mailing Lists

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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graphics problems after update from UCSF-Chimera64-1.5.3 to UCSF-Chimera64-1.6.2
by Dieter Blaas 21 Aug '12

21 Aug '12

Hi, I replaced the previous version of Chimera, UCSF-Chimera64-1.5.3 with the new one UCSF-Chimera64-1.6.2 on our cluster running Linux l22 2.6.32-131.17.1.el6.x86_64 #1 SMP Wed Oct 5 17:19:54 CDT 2011 x86_64 x86_64 x86_64 GNU/Linux whereas everything was perfect so far I now get the error message: 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 followed by a crash. This is annoying since I need the new version for compatibility with some sessions saved with the new version on another machine. Thanks a lot for hints, 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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a problem with silhouettes
by Alja Oblak 20 Aug '12

20 Aug '12

Dear Chimera users, I am trying to create an image for a publication using Chimera 1.6.1. Whenever I turn on "silhouette" dark spots appear on the screen and on the saved image. They seem totally random but they move along with the structure when rotated. When I zoom on them they look like small "umbrella-shaped" discs. The "show shadows" option is turned off. Does anybody know what are those spots and how to get rid of them? Thank you very much for any help. Regards, Alja Oblak

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how to use antechamber?
by 何永辉 16 Aug '12

16 Aug '12

Hello, Can you show me how to use the ambertool antechamber in Chimera? Thanks! Yonghui Dr. Yonghui He Central South University 932 Lushan South Road Changsha, China.

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em fit refinement
by Bala subramanian 15 Aug '12

15 Aug '12

Friends, I used "fit" command to fit a structure onto a EM map and obtained a list of fits. Now i want to choose the best fit and refine it further. I would like to know if there is any way to refine a fit produced by fit command in Chimera. Or can i use any other software for the same, which can take chimera's fit as input and refine it further. Thanks, Bala -- C. Balasubramanian

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Mountain Lion
by John (Jack) Johnson 13 Aug '12

13 Aug '12

Are there any issues with the current Mac version of Chimera (1.6.2) and Mac OS 10.8 (Mountain Lion)? Also, for a MacBook Pro (latest version) should one be using 32 or 64 bit version of Chimera. Thanks, Jack John E. Johnson Elden R. Strahm Professor of Structural Virology PHONE 858-784-9705 Department of Molecular Biology, MB31 FAX 858-784 -8660 The Scripps Research Institute EMAIL jackj(a)scripps.edu<mailto:jackj@scripps.edu> 10550 N. Torrey Pines Rd. La Jolla, CA 92037 http://johnsonlab.scripps.edu/ Virus Partcle ExploreR (VIPER) http://viperdb.scripps.edu/ ******************************************************************************** Olive Ireland PHONE 858-784-2947 Administrative Assistant EMAIL ireland(a)scripps.edu<mailto:ireland@scripps.edu>

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Elongating TMV capsid
by Jeremiah Gassensmith 13 Aug '12

13 Aug '12

Hello, I've downloaded the tobacco mosaic virus structure from the PDB and used Multiscale Models to build the biological unit. Unfortunately, only about 45 or so of the 2200 protein monomers show up. Is there a way I can multiply the biological unit to elongate the TMV structure? I don't need all 2200 monomers, but something a bit longer would be helpful. Thanks! Jeremiah Dr. Jeremiah J. Gassensmith Stoddart Mechanostereochemistry Group Northwestern University 2145 Sheridan Road Evanston, IL 60208-3113 Phone (W) +1(847)467-5936 Fax +1(847)491-1009

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Chimera inquiry: .py to .u3d conversion
by Will Jones 13 Aug '12

13 Aug '12

Hello, My name is Will. I'm a researcher at the University of Iowa. Our group has been using your Chimera software to visualize a model of our protein of interest. It's been very helpful but I've run into a small issue that I'd like to ask your advice on. I'm trying to convert the 3d image of the saved .py file into a universal 3D file (.u3d). I have tried several types of conversion software including polytrans/nugraph, 3DVIA Composer, and CS5 Adobe Photoshop with no success. Could you please tell me if conversion of .py to .u3d is possible, and if so how I might go about it. Thank you, I appreciate your time. Sincerely, Will -- Department of Biochemistry University of Illinois Urbana-Champaign Class of 2012

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Saving Images
by Hobbs, Merlin Eric 09 Aug '12

09 Aug '12

We are having trouble saving images to look a certain way. More specifically we are trying to make an image with the distance from a residue to a metal ion shown. The problem arises when we save the image the 'thickness' of the distance line doesn't change on the actual saved image. So no matter what the thickness is on chimera the image will always show the distance line as being less thick. Thanks Eric -- Merlin Eric Hobbs | Graduate Student, Biochemistry and Biophysics | Raushel Lab | Rm 2510 | Texas A&M University | College Station, TX 77842 | 979-845-9163 | eric0zero(a)tamu.edu

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Re: [Chimera-users] Rapid Access - a different question/request
by Eric Pettersen 08 Aug '12

08 Aug '12

On Aug 8, 2012, at 2:25 PM, Boaz Shaanan wrote: > OK Eric, thanks. I'll wait for the scroll bar since my window is already stretched to the limit. Okay, there will be a scrollbar in tonight's daily build. Worked fine in my tests. Speak up if it turns out I botched something! --Eric

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