- Chimera-users - RBVI Mailing Lists

Difference maps
by Katrina Lexa 01 Sep '10

01 Sep '10

Hello, I'm wondering whether it is possible to take the absolute value of a difference map created by the vop subtract command? Otherwise, so far as I can tell, the negative values which should be relevant I can't see because they just show up as a giant box. Thank you for your help, Kat

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PDB opens distorted
by Francesco Pietra 27 Aug '10

27 Aug '10

Hi: I have drawn a slightly modified small peptide (terminal phenylalanine changed to phenylalanine-amide) with an old, efficient package (PCMODEL). I have drawn from from either amino acid templates or atom-per-atom and then saved as pdb. In case of drawing atom-per-atom, I have edited the residue names, changing UNK to the appropriate standard amino acid name, except phenylalanine-amide, named PHA). Opening the pdb file with an editor, the atoms are often scattered, not sequentially grouped together for a given amino acid. Well, both the non-edited and the edited pdb files open correctly with either PCMODEL of VMD, not with CHIMERA. In the latter case, incorrect bonds between the atoms are seen, and the molecule is compressed. Deleting all CONECT generated by PCMODEL was even worse for CHIMERA. With non peptidic molecules I never went into such troubles using the same packages. Thanks for suggestions how to rearrange the pdb for CHIMERA. francesco pietra

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problems loading .mtz files
by rjoshi＠purdue.edu 25 Aug '10

25 Aug '10

Hi, i am having problems loading electron density files from CCP4 and Phenix. The error message reads "Bad MRC grid size (129737328,-319356160,1145110528)". Please advise. Cheers Rakesh Graduate student Dept.of Biochemistry Purdue University

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volume viewer question
by Boaz Shaanan 25 Aug '10

25 Aug '10

Hi William, The way I go about the sigma level contouring in Chimera, though it's somewhat ham-fisted but perhaps less complicated than Tom's suggestion, is to contour the region of interest at the desired sigma level in Coot or O and then play with the contouring in Chimera until both maps look as similar as possible (the maps rarely look identical for technical differences in the contouring techniques, I think). It works. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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volume viewer question
by William Snee 24 Aug '10

24 Aug '10

Hello, I am trying to make an electron density figure using chimera and need to contour the F0-Fc map to 3 sigma. How can you determine the sigma level displayed with the volume viewer? The levels appear to be different than that observed when using coot or Xtalview. Thank you, William Snee

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Chimera and Sparky
by Hagn, Franz 24 Aug '10

24 Aug '10

Dear all, I am trying to run Chimera connected to Sparky for NMR NOE visualization. I am using the latest Sparky MacOSX distribution (for 10.4) and the last built of Chimera which came out today on a MacOSX 10.6 Intel. When I start Chimera within Sparky, I get a bunch of error messages. Does anybody know which Chimera runs with the latest Sparky? Thanks, Franz -- Franz Hagn, Ph.D. Department of Biological Chemistry & Molecular Pharmacology, Room C1-103 Harvard Medical School 240 Longwood Ave, Boston, MA 02115 Tel: +1(617)432-3211 Fax: +1(617)432-4383 --- Franz Hagn, Ph.D. Department of Biological Chemistry & Molecular Pharmacology, Room C1-103 Harvard Medical School 240 Longwood Ave, Boston, MA 02115 Tel: +1(617)432-3211 Fax: +1(617)432-4383

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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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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 List posting
by Hagn, Franz 12 Aug '10

12 Aug '10

Franz_Hagn(a)hms.harvard.edu

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Chimera startup options
by Beale, John 12 Aug '10

12 Aug '10

I have a new installation of Chimera on a Linux box. I am working with a protein/nucleic acid complex. When I start the program with "chimera file.pdb" the ribbon representation of the structure is shown. Also, a plank representation of the nucleic acid is shown. I have to hide the ribbon and select "Actions -> Atoms/Bonds -> Show" to see the atoms. Can someone tell me how to change the startup options so that the ribbon and planks are not automatically generated and that the atoms/bonds are shown by default? 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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