- Chimera-users - RBVI Mailing Lists

Problem adjusting sphere quality in script
by Marhoefer, R (Richard) 16 Mar '09

16 Mar '09

Dear Chimera Users, I want to adjust the quality of spheres, cylinders and ribbons in a script. From the moviemaking tutorial script I learned that I must use some lines of Python. Therefore, I used the code as found in the example: import chimera chimera.LODControl.quality = 20 When I open this script like in the tutorial, the value of "subdivision quality" in the "Effects" panel is indeed set to 20. However, the quality of spheres and cylinders remains untouched. From that point in time any further modifications of the value in the "Effects" panel do not have any effect. If I change the value of "subdivision quality" in the "Effects" panel before opening the Python code, anything works fine. Did anybody succeed with changing the sphere quality in a script? Kind regards, Richard Mit freundlichen Grüßen / With kind regards Dr. Richard Marhoefer Senior Scientist BioChemInformatics Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: richard.marhoefer(a)sp.intervet.com Phone: +49 (6130) 948 204 Fax: +49 (6130) 948 517 Mobile: +49 175 723 081 4 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. --------------------------------------

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command line
by Sirano Dhe-Paganon 16 Mar '09

16 Mar '09

After entering a command in the "command line" of UCSF-Chimera, I would like the command that I pasted to disappear. Currently, it does not disappear; how can I make it disappear after I press the enter button?

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Chimera needs your vote.
by Nir London 16 Mar '09

16 Mar '09

There is a poll going on at the macromolecular modeling blog "What is your favorite molecular viewer?" http://rosettadesigngroup.com/blog/284/what-is-your-favorite-molecular-view… PyMOL is currently at the lead, but you might make the difference, go ahead and show your support for Chimera (or choose one of the other viewers if you like them more) but most importantly drop a comment as to why YOUR viewer is the best. Disclaimer: for fairness, similar messeges are sent to the other competitors mailing lists as well, but we like yours the most ;) Nir London. Rosetta Design Group. http://rosettadesigngroup.com/blog/

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centering on an atom
by Sirano Dhe-Paganon 16 Mar '09

16 Mar '09

In UCSF-Chimera, I would like to center on an atom of a molecule without zooming-in towards the atom. I found the "focus" command, which centers the atom, but the command includes a zooming-in step; is there a "focus" or "center"-like option that does not zoom-in? Also, most visualization programs have a simple, one-click mouse-button to center on an atom; I cannot find this option in UCSF-Chimera. Sirano

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Re: [Chimera-users] window size
by Elaine Meng 13 Mar '09

13 Mar '09

Hi Jean-Paul, For a more reliable response, please send questions to chimera- users(a)cgl.ucsf.edu rather than to me directly -- I might be out (sick or vacation), or others may know the answer when I don't! There is no preference for window sizes and locations. However, there is a startup option "--geometry" for the main window (but not other tools, sorry): <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#geometry> How to specify startup options depends on your type of computer: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/startup.html> Some related things... After you start Chimera, you can use the "windowsize" command to specify the pixel dimensions of the main window. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/window.html> If you save a session, it should restore with the same main window size. I don't think the location is saved, however. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sessions.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 13, 2009, at 11:16 AM, Jean-Paul Armache wrote: > hello, > i have a question. is there a way of saving the window sizes and > windows positions in chimera ? whenever i start chimera the default > all the windows have always the same position and sizes. i always > adjust it to the same position and size, but maybe there is a way to > save it as a preference ? i checked the preferences file, nothing > there. > thank you, > best regards, > jean-paul armache

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chimera help
by Terrance Chiang 11 Mar '09

11 Mar '09

Hi, I've been trying to make an electrostatic potential map for the protein that I'm working on, but there seems to be some error with the file when I try to open it. I was wondering if you could help me with this. The error says: Missing "object 1 class gridpositions counts <l><m><n>" header line I also need help with using the pdb2pqr service that can convert files from pdb into apbs. Perhaps my error lies there. Thanks, Terrance Chiang

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Atoms outside volume
by Tom Goddard 10 Mar '09

10 Mar '09

Hi Tsutomu, I guess you want the atoms outside a given contour level of the volume. There is a Chimera keyboard shortcut "oa" (outside atoms) to select those atoms. If you don't use shortcuts (Tools / General Controls / Keyboard Shortcuts) you can run them as ordinary Chimera commands using the "ac" command: volume #0 level 2.5 select #1 ac oa These 3 commands set the contour level for map #0, select all the atoms in PDB model #1, then run keyboard shortcut oa which changes the selection to just those outside the contour. If you have multiple maps open, the "oa" shortcut is using the highlighted one in the volume dialog. You can write the selected atoms to a file if desired with menu entry Actions / Write List.... If you really want atoms outside the volume bounding box, then just use a threshold less than the smallest data value (range shown in volume dialog). Tom Tsutomu Matsui wrote: > Dear Tom, > > My name is Tsutomu Matsui, a postdoc in Jack Johnson Lab at Scripps > Resaerch Institute. I love Chimera very much. I would like to select > all atoms inside or outside a volume file (density map). Is it possible? > > Thank you very much, > Tsutomu >

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center of the molecule
by Bala subramanian 10 Mar '09

10 Mar '09

Dear Friends, How can i get the x,y,z of the center of the loaded molecule in chimera. While i do box generation generation for DOCK program, i want to tell the script to construct box by considering the x,y,z center of the molecule. Thanks, Bala

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Copy a pdb display configuration to another pdb model
by Tom Goddard 10 Mar '09

10 Mar '09

Hi Xiangan, I've added a new Chimera command "mcopy" to copy colors, display styles, coordinates and other settings from one molecule to another. mcopy #0 #1 will copy the colors, display styles (ribbon, stick, sphere, ...), and visibility (which atoms/residues shown) from molecule #0 to molecule #1. To copy other attributes such as atom coordinates, molecule placement (transform), or labels use the "settings" option: mcopy #0 #1 settings lxp copies just atom/residue labels, atomic coordinates and placement. The recognized settings are: c = color, s = style, v = visibilty, l = labels, x = coords, p = placement, a = all. The default is "csv". This command will be in tonight's Chimera builds. http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Tom Xiangan Liu wrote: > Tom, > I asked you a question in BPS meeting regarding the implementation of > copying a display configuration of a pdb file to anoth pdb with the > same sequences. Did you get chance to implement it into chimera daily > release? If yes, what is the command. If not, can you send me the > corresponding python codes to me? > Thanks, > > Xiangan >

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Atom Replacement
by Warren Menezes 10 Mar '09

10 Mar '09

** High Priority ** Hi! I was wondering if it is possible to replace a Selenium atom in a protein with a Sulfur atom? The reason is because Sulfur has parameters. Thanks! Warren M Chicago

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