- Chimera-users - RBVI Mailing Lists

stupid problem
by Hartzell Jr., Criss 26 Nov '12

26 Nov '12

Until recently, FAVORITES > SEQUENCES only opened a new window showing the sequence. Since I upgraded to version 1.6.2, this not only opens the sequence window, it also automatically adds a new model for each sequence to the model panel and opens a new instance of the structure in the graphics window. How do I stop this? I just want the sequence window. Thanks. ________________________________ 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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Cluster list
by Rebecca Swett 26 Nov '12

26 Nov '12

Is there any way to get a list of all the members of each cluster when using the tool Ensemble Cluster? Basically i'm looking to run the clustering bit, and then write a list -cluster 1 members:1-3,4-8, etc. for all clusters produced. Anyone out there have any suggestions? Thanks for anything you've got. I think I could get it by manually going through: choosing a cluster, selecting it, and then using the write list function with a custom identifier, but i've got a lot of these to handle. -- Rebecca Swett Wayne State University 357 Chemistry Detroit, MI 48201 Lab Phone 313-577-0552 Cell Phone 906-235-0768

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how to add misiing proline between H2 and H3
by amna khan 26 Nov '12

26 Nov '12

hi, i am new to chimera when i minimize my pdb structure, it gives the following error The following residues had non-integral charges: DA 1.D -0.3079 DA 19.D -0.6921 PRO 43.P 0.376 1 model(s) had non-integral total charge Details in reply log Residue #0:43.P (PRO/proline) is missing atoms H_2 and H_3 i am not able to minimze the strcuture due ti this error , please help me how to remve this error regards

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Mutation of residue
by Tijesunimi Odebode 26 Nov '12

26 Nov '12

Hello all, I am new to Chimera and I am trying to change a serine in the sequence of my protein to a leucine. Is there a way of doing that in Chimera? Thanks in advance for the help. TJ

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Quadro versus GTX graphic cards
by Oliver Koch 23 Nov '12

23 Nov '12

Dear Chimera users, I want to buy new computer for my lab and I'm not sure which graphic cards I should buy. Is it really necessary to invest in expensive nvidia quadro graphic cards in comparsion to the nvidia gtx consumer cards? My private desktop computer has a GTX570 and everything is working fine. I searched the internet and talked to a lot of people, but nobody could say if you really recognize the difference in your daily work. The background: I want to use the computer for modelling (Chimera, Moe, ...) with two screens and stereoview using nvidia 3d vision. The OS will be linux (presumably scientific linux). I would be very happy if you can share your opinion. Many thanks Oliver -- Dr. Oliver Koch Junior Research Group Leader "Medicinal Chemistry" Chemical Biology Faculty of Chemistry Technische Universität Dortmund Otto-Hahn-Straße 6 44227 Dortmund EMail: Oliver.Koch(a)tu-dortmund.de

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Movie with multiple models
by Benefield, Desiree A. 20 Nov '12

20 Nov '12

Hello again, I have a 3D reconstruction volume file. I'd like to show the initial model as a solid surface, then as a mesh surface, and then as the mesh surface with crystal structures. Can you recommend the best way to approach this? Specifically, I am uncertain as to what command will help me accomplish this and/or if I need different chimera files for each form of the model... Very sorry to keep bothering you. I appreciate the advice. Desiree

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Coulombic coloring
by Mock, Sebastian 20 Nov '12

20 Nov '12

Hi Chimera Team, is it possible to color the active site of an enzyme let's say green after the coulombic coloring, without losing the last-mentioned? The coulombic coloring disappears when I try to color specific positions in the structure to green. Thanks in advance Sebastian

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Question about tilting a structure in a movie
by Benefield, Desiree A. 20 Nov '12

20 Nov '12

Hello all, I am a new Chimera user and interested in using the program to create a movie of one of my molecular structures. I have been using some basic commands (turn, rock, etc.) but I would also like to be able to tilt my molecule. For example: tilt forward 45 degrees and tilt back to the original position. I can get the model to tilt by using the command line: turn x 1 45 however, I can't figure out how to make the model return to its original position smoothly. I can use the reset command but that looks a little disjointed. Any advice or suggestions would be greatly appreciated. Thanks, Desiree

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coil representation thickness
by Evan Kantrowitz 20 Nov '12

20 Nov '12

Hi, I am trying to setup a python script to display a series of similar structures. I would like each shown as just a thin coil like licorice but much thinner. I can get the representation I want by using custom scaling in the Ribbon Style Editor and setting everything to 0.1. Is there a command line command to set the thickness of licorice. Else, how can I do give the scaling commands used in the Ribbon Style Editor from the command line or what python command(s) will do it. Thanks in advance. Evan ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu<mailto:evan.kantrowitz@bc.edu> Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow<http://www2.bc.edu/~kantrow> Chestnut Hill, MA 02467 -------------------------------------------------------------------

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Problems installing and running chimera on opensuse 12.1
by Visvaldas K. 20 Nov '12

20 Nov '12

Hi all, I'm having problems after the opensuse (gnome desktop) upgrade to the 12.1 version. I can go on for hours how great this new gnome desktop is *NOT*, but that's not the main issue here. During installation, the messages are as follows: Downloads% ./chimera-alpha-linux_x86_64\(1\).bin UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Original path: '/home/visvaldas/Downloads' inflating: chimera_install_vautEs/installer inflating: chimera_install_vautEs/chimera.bin Enter install location: ~/.local/UCSF-Chimera64-2012-11-14 Extracting files. This may take a few minutes. Executing command: './chimera.bin -q -d /home/visvaldas/.local/UCSF-Chimera64-2012-11-14' UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://www.info-zip.org) Install desktop menu and icon? yesyes Traceback (most recent call last): File "/home/visvaldas/.local/UCSF-Chimera64-2012-11-14/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/home/visvaldas/.local/UCSF-Chimera64-2012-11-14/share/chimeraInit.py", line 594, in init import chimera File "/home/visvaldas/.local/UCSF-Chimera64-2012-11-14/share/chimera/__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: libbz2.so.1.0: cannot open shared object file: No such file or directory ERROR in chimera_final_install: unable to install desktop icon: result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_vautEs' Installation is done; press return. This was using the November 14 version of Chimera. libbz2 error happens also during the run (I don't care much about icon problem). visvaldas% ~/.local/UCSF-Chimera64-2012-11-14/bin/chimera 1HVR.pdb Traceback (most recent call last): File "/home/visvaldas/.local/UCSF-Chimera64-2012-11-14/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/home/visvaldas/.local/UCSF-Chimera64-2012-11-14/share/chimeraInit.py", line 594, in init import chimera File "/home/visvaldas/.local/UCSF-Chimera64-2012-11-14/share/chimera/__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: libbz2.so.1.0: cannot open shared object file: No such file or directory Thank you for your attention, and many thanks. Vis

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