- Chimera-users - RBVI Mailing Lists

ValueError: dimensions too large
by Josh Kacher 24 Aug '10

24 Aug '10

I am trying to use the volume eraser, but whenever I click erase, I get a Chimera Error box come up that says: ValueError: dimensions too large. File "C:\Program Files\Chimera\share\VolumeViewer\volume.py", line 1085, in region_grid m = zeros(shape, d.value_type) Does anyone know how to avoid this? I tried shrinking the volume eraser size. I also tried installing Chimera on a different computer to see if that was the problem, but it still isn't working. Thanks, Josh

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writing MRC maps
by Dougherty, Matthew T 24 Aug '10

24 Aug '10

I have an MRC map that is 800^3. I do a color zone and split the map, generating eight maps, each 800^3. The first of the split maps I throw away, the volume of interest of the other seven maps is 50^3 each. How do I save the seven maps not at 800^3, but reduce their size to 50^3? thanks, Matt

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sausage view
by lalit.deshmukh＠huskymail.uconn.edu 24 Aug '10

24 Aug '10

Hello, Is there anyway to generate a sausage view (see the attached image) by using Chimera? My apologies if I missed something/or this has been discussed before. Thanks in advance, Regards, Lalit

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Ringer: A program to detect molecular motions by systematic X-ray electron-density sampling
by Terry Lang 20 Aug '10

20 Aug '10

The Alber lab at UC Berkeley is pleased to release of the code for Ringer version 1.0 (http://ucxray.berkeley.edu/ringer.htm) which depends on Chimera. Ringer is a program to detect molecular motions by systematic X-ray electron-density sampling. The aim of Ringer is to go beyond static structural snapshots of proteins by uncovering structural ensembles in X-ray electron density. This information can reveal not only which parts of proteins are flexible and which parts are rigid, but it also can define alternate conformations that may be important for function. Alternate conformations of binding sites also may afford additional targets for drug design. The Ringer method is described in Lang et al. /Protein Sci/. 2010 Jul; 19(7):1420-31 <http://www.ncbi.nlm.nih.gov/pubmed/20499387>. An application of Ringer, determining the structural underpinnings of the side chain dynamics critical for the function of the enzyme proline isomerase, was published in Fraser JS et al. /Nature/. 2009 Dec 3;462(7273):669-73 <http://www.ncbi.nlm.nih.gov/pubmed/19956261>. Ringer is freely available to academics. -- PaulaTherese Lang Postdoctoral Scholar Alber Lab, UC Berkeley http://ucxray.berkeley.edu/ringer.htm

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Question regarding Chimera Measurements
by Shahmoradian, Sarah H 19 Aug '10

19 Aug '10

Hello, This is an urgent question and your help would be appreciated. I am trying to find a way to perform measurements in my tomogram volume file (.rec file). I tried using the "Distances" option under Tools --> Structure analysis, but this requires two "atoms." My tomogram does not depict at the atomic resolution and I would like to measure the distance between one area on my tomogram density and another area on the tomogram density. These measurements would be through a 3D section. Could you please let me know how I could do this? Furthermore, I have a question about the scale bar -- when the program generates a default scale bar, how does the program assign the default value to the scale bar size? Does it read the header info from my tomogram file? I am concerned because when I change the label name from Angstrom to nanometers, the scale bar size stays the same-- how then, would I be able to assign an accurate scale bar that would change accordingly with the alterations in scale (Angstrom to nm, etc)? Please let me know if I need to clarify further. Your assistance would be appreciated! Sincerely, Sarah Shahmoradian Molecular Physiology and Biophysics (Baylor College of Medicine) Pre-doctoral fellow, Nanobiology Interdisciplinary Graduate Training Program (Rice University)

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Positioning of water molecules in a protein
by Beale, John 19 Aug '10

19 Aug '10

Is there a way to use Chimera to determine what atoms/groups in a protein are closest to a particular water molecule? I have an x-ray structure that is solvated. I would like to determine the positions of the water molecules in the x-ray structure and compare these to the water molecule positions after molecular dynamics. 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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Stereo monitors
by Jeremy Swan 18 Aug '10

18 Aug '10

Hi all, Any recommendations on stereo monitors for chimera on a pc? Thanks! -Jeremy Sent from iPhone

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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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