- Chimera-users - RBVI Mailing Lists

morph problem
by Andres Palencia 02 Mar '11

02 Mar '11

Dear Chimera Users, I am trying to morph the complex1 and complex2 from the same system (protein-RNA) to make a video monitoring the conformational changes. As complex 1 is missing one domain and a helix (not visible in the crystal structure), I need to remove these parts in complex 2 to have an equal number of atoms in both complex and could morph it. The resulting video is not so nice because shows the gaps corresponding to the missing part. So, to avoid that, I have modelled the missing part in the complex 1 to have the same atoms, and afer morph it again to make the video, but this is not working. In the transition between complex 1 and complex 2, the RNA encounter one helix on the way that needs to move out to let the RNA to get the position observed in complex 2. If I take out this helix, the video can perfectly be done, but still is not perfect because show gaps. Anybody could give an idea in how to solve the problem? We need the video to include in a publication,. Thanks in advance, Andrés Palencia -- Andres Palencia, PhD Protein RNA Group EMBL Grenoble Outstation 6 rue Jules Horowitz BP181, 38042 Grenoble Cedex 9, France email: palencia(a)embl.fr phone: + 33 (0)476 20 7860(office)/ + 33 (0)476 20 7014(lab) fax: + 33 (0)476 20 7199 http://www.embl-grenoble.fr/

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3-D
by Jason Bouvier 02 Mar '11

02 Mar '11

Hi, how do I view proteins in 3-D in Chimera? And would I use standard 3-D glasses or are special ones required? I viewing in stereo with some old 3-D glasses that I had around but to no avail. Thank you. Cordially, Jason Bouvier Jason Bouvier | Graduate Student, <http://mcb.illinois.edu/departments/biochemistry/> Biochemistry | <http://www.life.illinois.edu/gerltlab/research.html> Gerlt Lab | <http://www.igb.illinois.edu/> Institute for Genomic Biology | Rm 3200 | <http://illinois.edu/> University of Illinois at Urbana-Champaign | 1206 W. Gregory Dr. | MC-195 | Urbana, IL 61801 | office 217.333.2673 | lab 217.333.2699 | <mailto:jbouvier@illinois.edu> jbouvier(a)illinois.edu

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Problem with Nvidia Quadro FX 880M and Stereocopic view
by Veli-Pekka Kestilä 01 Mar '11

01 Mar '11

Hello, I have problem with Nvidia Quadro FX 880M and Stereoscopic view. When I switch the stereoscopic view on in Chimera it gives me following error: stereo viewing (Unable to find hardware stereo support (couldn't choose pixel format Couldn't configure togl widget)). I have installed the Quadro drivers version 259.57 in Windows 7 64bit. And separate 3D driver for Quadro. Greetings, Veli-Pekka Kestilä -- University of Helsinki / Institute of Biotechnology / veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3

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chimera ?
by Alexander Spyros Maris 01 Mar '11

01 Mar '11

Hi, I was attempting to start part of the tutorial by fetching "1d86" from the PDB on my windows PC when I got the error message "No connection because the target refused." Do you know how I can fix this? Thanks! -- Alex Maris

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Internal water molecules
by Beale, John 28 Feb '11

28 Feb '11

Hello, Is it possible, in Chimera, to select only the internal water molecules of a protein structure? I need to find out how many water molecules enter the protein structure from the outside during a molecular dynamics simulation. Thanks! John John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale(a)stlcop.edu<mailto:jbeale@stlcop.edu>

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hem group
by "dr. R�szer Tam�s" 28 Feb '11

28 Feb '11

Hello, I would like to add HAEM group to a protein reconstructed from pdb data. I am working on Windows platform. Could you please help me how can I do that? many thanks Tamas

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How to
by M. Amin Arnaout 28 Feb '11

28 Feb '11

I am running Cimera 1.5.2 on Mac. I am now unable to show a cabonyl O, N or CA of a residue while ribbon is also displayed. Could do that in the earlier version. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Re: [Chimera-users] [chimera-dev] clashes and contacts with hidden models
by Elaine Meng 28 Feb '11

28 Feb '11

On Feb 28, 2011, at 5:28 AM, Elisabeth Ortega wrote: > > I have a question related to the calculation of the clashes between two (or more) models. What I have to do to count only the clashes of the Active or Displayed models? I mean, if I have 3 models in the model panel and I only want to calculate the clashes between the models 1 and 2 without close the model 3, what I have to do? > Hi Elisabeth, With either the graphical interface of Find Clashes/Contacts or the command findclash, you can specify which two groups of atoms to examine for clashes. The remaining atoms will be ignored. I believe it doesn't matter whether the atoms are displayed or active. With the command, it would be something like findclash #1 test #2 [other options] Another example: findclash ligand overlap -0.4 hb 0 test aromatic Use command "help findclash" to see the manual page, or view it here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> With the GUI, the procedure is slightly different: you would select one group (say #1), click Designate, choose option "second set of designated atoms", select the second group (say #2), click "Designate selection as second set", Apply. Click the Help button to see the manual page, or view it here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas…> This is more of a chimera-users(a)cgl.ucsf.edu question (how to use Chimera) than chimera-dev (programming related to Chimera), so I'm also CC-ing the former list. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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suggestion: sym option
by Dougherty, Matthew T 25 Feb '11

25 Feb '11

add an SYM command option to specify the model number of the resulting model Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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morph shape/bild objects
by Do-Nyun Kim 25 Feb '11

25 Feb '11

Hello, I'm using shapes in bild format to make spheres and cylinders in Chimera. Is there a way of morphing these shapes, spheres in one conformation to spheres in another conformation? Thanks you. Best regards, Do-Nyun Kim.

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