August 2010 - Chimera-users - RBVI Mailing Lists

2D image contour plot using Chimera
by Yao Cong 16 Aug '10

16 Aug '10

Dear Chimera developer, I was wondering that is there any way that I can use Chimera to do a 2D image contour plot? Do I need some extra plug in or tools? Thanks a lot, Yao ------ Yao Cong, Ph.D. Research Associate, National Center for Macromolecular Imaging, Baylor College of Medicine, One Baylor Plaza, Alkek Building N420-BCM125, Houston, TX 77030 Tel:713-798-6989 Fax:713-798-1625 Email: cong(a)bcm.edu

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representing additional residues over ribbons
by Irene Newhouse 16 Aug '10

16 Aug '10

When I try repr sphere :64 or repr stick :64 over the default presentation of my protein in ribbons [the heme group is in sticks, as are automatically selected residues in close proximity], as suggested in today's user mail, it doesn't work. It only seems to work if all atoms of the protein are displayed. I can only reset the display mode of the residues Chimera has chosen to show in addition to ribbons using these commands on the default mostly-ribbon display. How do I get the protein mostly in ribbons with a few residues in stick or ball & stick? While I haven't worked through the entire tutorials referenced in today's mail, the examples of repr shown early on do not do this; they start from a display of all the protein's atoms. Thanks! Irene Newhouse

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displaying specific residues
by Elaine Meng 16 Aug '10

16 Aug '10

On Aug 12, 2010, at 7:04 AM, Reza Heidari wrote: > How can i display just some of residues (in form sphere) on a protein (in form ball & stick), for example: Trp38, Val66, Ala80. Please help me, thanks a lot. Hi Reza, There are many ways to get the same final result. I will give only two examples here. You may want to look at the "Getting Started" tutorial and other tutorials for more information: <http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html> <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html> Example 1: Show the command line by choosing from menu: "Favorites... Command Line" If you don't want any ribbon, use command: ~ribbon Show all protein atoms/bonds and hide others with command: show protein (to show ALL atoms/bonds including nonprotein, use command: display) Change style of all atoms/bonds to ball&stick: repr bs Change style of specific residues to sphere: repr sphere :38,66,80 (other commands such as color, display, ... also take these residue lists) Example 2: If you don't want any ribbon, use menu: Actions... Ribbon... hide Show all atoms/bonds with menu: Actions... Atoms/Bonds... show ( If there is water and you want to hide it, menu: Select... Structure... solvent menu: Actions... Atoms/Bonds... hide menu: Select... Clear Selection ) Change style of all atoms/bonds with menu: Actions... Atoms/Bonds... ball & stick Display sequence window with menu: Favorites... Sequence Click on Sequence window top bar, then inside that window, use mouse to choose residue 38; then it will be selected in the main window Change selected residue to sphere with menu: Actions... Atoms/Bonds... sphere Go back to Sequence window, choose next residue, etc. For the future: general questions should go to chimera-users(a)cgl.ucsf.edu (chimera-dev is for programming questions) and include a brief description in the Subject line of the mail. 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

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OpenGL misconfiguration & Nvidia
by Hernando Sosa 14 Aug '10

14 Aug '10

Hi I recently installed the proprietary Nvidia driver in a Linux box (OpenSuse 11.3 64bits) and now every time that chimera start there is a warning dialogue saying that there is an OpenGL misconfiguration detected. If I ignore the warning (press YES to continue) chimera seems to run fine. So my question is how can I either fix the problem or get rid of the warning dialogue? At the terminal the following message is displayed when starting chimera >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Error: API mismatch: the NVIDIA kernel module has version 256.44, but this NVIDIA driver component has version 256.35. Please make sure that the kernel module and all NVIDIA driver components have the same version. <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< I am not sure which one is "this NVIDIA driver component" that I need to fix and why it was not updated when installing the proprietary driver. Thanks System details: Chimera version: production release 1.4.1. (for 64 bit Linux) Card: Nvidia geforce GT 230 Processor: AMD Phenom X6 1090T OS: 64bit Linux OpenSuse 11.3 -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa(a)einstein.yu.edu -----------------------------------

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Re: [Chimera-users] surfnet - separating clefts from cavities
by Elaine Meng 12 Aug '10

12 Aug '10

Hi Irene, Unfortunately surface models aren't directly saved in sessions. Molecular surfaces and volume isosurfaces are effectively saved in that they are regenerated from the underlying atomic or volume data when the session is restored. Some other surface-generating tools are also integrated with sessions, but not Surfnet. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sessions.html#whatsaved> I should mention that limitation in the docs. Experiments also reveal that "Surfnet Selection" is ignoring my atom specification of "protein" -- it seems to be using all atoms. However, I can get the desired result by using "Surfnet Interface" instead and specifying "protein" as both the ligand and receptor. This problem with Surfnet Selection is in both the release 1.4.1 and the current daily build, and I will be reporting it as a bug. If the volume method (alternative (B) in my chimera-users message earlier today) had been used, that surface would be restored along with the saved session. There is still the drawback that it "forgets" it has been split and partially hidden. Upon session restore it is regenerated anew and shown in its multiblobbed entirety. Drats, foiled again! Sorry about that, 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 Aug 12, 2010, at 4:05 PM, Irene Newhouse wrote: > Thanks for your response! I've gone on ahead, manually deleting the clefts. > Also, is there a way to save the computation? When I did a 'save session' > & brought it back, the surfnet calculation wasn't there. The calculation itself > is quick, it's the hiding the bits you don't want to show that's a pain to regenerate...

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surfnet - separating clefts from cavities
by Irene Newhouse 12 Aug '10

12 Aug '10

I've been random-walking my way with surfnet, starting from the stand-alone version. I haven't been able to get the output file I need for displaying via RasMol, & while I was googling for cures to that, I discovered the surfnet plugin to Chimera, hurray. I have a protein with several internal cavities, plus many more surface clefts. Has someone worked out an efficient way to display only the internal cavities? From my previous mucking about with the stand-alone, I already had a 'cavity atoms' pdb-format file which I loaded as model 1 & used that. However, generating the cavity atoms file involved considerable work by hand. At the moment, I can picture splitting the surfaces [using directions in the chimera user archive] & deleting all the surface ones. This is also a fair amount of manual labor - 50 blobs are generated & only 9 are internal. I have other proteins in this family to analyze, & they're probably similar. Thanks for any advice! Irene Newhouse

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Re: [Chimera-users] unsubscribe
by Elaine Meng 12 Aug '10

12 Aug '10

Hi Arne et al., Today there is a glut of messages that had been held up in our system over the last several days. Apologies, and now that we know the problem, it should not recur. Those who wish to unsubscribe can do so at <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> Best, 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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Chimera on Linux
by Jay Brown 12 Aug '10

12 Aug '10

Dear Chimera: I successfully installed Chimera on a Linux machine, and it worked as expected for about an hour. Then it began shutting down any time I tried to rotate a volume image (e.g. emd_1015.map). Nothing comparable happens with the version I have running on a PC. Is there something about Linux I need to know? Thanks. -Jay Brown Jay C. Brown Department of Microbiology University of Virginia School of Medicine 1300 Jefferson Park Ave. Charlottesville, VA 22908 Email: Jcb2g(a)virginia.edu Phone: 434-924-1814 http://people.virginia.edu/~jcb2g/index.htm

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3d chimera viewing with nvidia vision and geforce 220
by William Tieu 12 Aug '10

12 Aug '10

Dear chimera users I am having problems with getting the sequential stereo view on chimera 1.4.1 windows 32bit. The error i'm getting is: Unable to turn on stereo viewing Unable to find hardware stereo support (couldn't choose stereo pixel format Couldn't figure togl widget) I recently obtained a samsung 2233RZ monitor, 3d nvidia vision and using a nvidia geforce 220. My question is, whether the problem is because of using a geforce over a quadro? and whether there is a way to resolve this problem with a geforce card. Or is there another reason for the error message. Thank You William Tieu Department of Chemistry and Physics Adelaide University

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how is the threshold calculated?
by Mitul Saha 12 Aug '10

12 Aug '10

Hi! In Chimera's Volume viewer, how is the default density threshold computed for a given loaded 3D density map? Thanks, MS

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Chimera-users August 2010