- Chimera-users - RBVI Mailing Lists

bug reporting broken for the last day or so
by Eric Pettersen 18 Oct '11

18 Oct '11

Hi all, If you used "Report A Bug" (or the automatic bug-reporting dialog) in the last day or so, the bug report didn't get properly handled by our site despite the dialog itself saying that the bug report was successfully submitted. So if you need help with a problem contained in such a report you will need to resubmit it. Sorry! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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sequencial fitting
by Guimei Yu 18 Oct '11

18 Oct '11

Hi Sir or Madam, I am trying the sequential fitting in Chimera following the on-line video provided in your Homepage. But when I tried to use the "fit" command, it couldn't be recognized by the program. What's the possible reason about this? Is it because of the version? Thanks a lot! Sincerely, Guimei Yu Graduate Purdue University

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pH-dependent surface potential
by Dieter Blaas 15 Oct '11

15 Oct '11

Hi, Is there an (easy) way of displaying the surface potential at different pH values within Chimera? The Chimera-contained Coulombic Surface Colouring does not appear to take into consideration the pH-dependent protonation state (as far as I understand it assumes pH 7). Thanks a lot for hints, Dieter -- ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories. Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Connect and align duplicated models
by Joe Ping-Lin Hsiao 14 Oct '11

14 Oct '11

Hi, I are trying to use Chimera to produce duplicates of one fibrinogen, rotate and move them, and concatenate together in a certain way. The fibrinogen looks like this (http://dl.dropbox.com/u/3757507/chimera1.png) I want to duplicate the model, and connect them in a chain (http://dl.dropbox.com/u/3757507/chimera2.png) The second image shows only two instances, but there will be more. Currently I do it by hand, including rotating and aligning them in correct z positions. But it take a lot of time to do it because the duplicates generated by using Tools/Higher-order structure/Unit Cell are not in the same plane. I have to look back and forth in different directions to make sure them are aligned. So I are wondering is there any way to automate this process, such as apply the previous transformation to a new duplicate? Thanks, Joe

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Gasteiger charge
by Ibrahim Moustafa 13 Oct '11

13 Oct '11

Dear Chimera developers: I want to assign Gasteiger charges for a ligand, as a preparative step for docking. The ligand is GTP, extracted from a protein complex structure. I wanted to add the Gasteiger partial charge, and explicitly chose to have a total charge of ³-4² on the ligand molecule. However, the program assigned partial charges that sum to total charge of ³-2² instead of ³-4². Any idea why the program assigned the Gasteiger partial charges incorrectly, ignoring the input total charge on the ligand. Thanks in advance for your help. Regards, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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how to display specific residues and atoms in chimera
by Abir 11 Oct '11

11 Oct '11

Hello, I am new to chimera. I am trying to make an animation of an actual reaction. I have the frames saved as pdbs. I guess one can use the MD movie tool to make the animation in chimera. However, I want to show only specific residues and atoms from my active site in the movie and not the entire system (my system is a ribozyme). I played with chimera for a while, but could not figure out how to do that. It will be great if I get some help regarding this issue. Thanks a lot. Regards, Abir

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Building Togl with 8.6b2
by Clifford Yapp 07 Oct '11

07 Oct '11

I've been trying to compile Chimera's latest Togl against the most recent 8.6b2, and I'm not quite seeing how to go about it. A straight configure doesn't seem to find GL/gl.h... does it require use of the GNUmakefile in the toplevel? That file seems to need Mesa - can this version of Togl be built without it? Should I be pointing the configure to the unix dir or the macosx dir when doing the Aqua build? Also, has anyone tried running the Togl gears demo with the NSOpenGL based version of Togl? Does it work? Cheers, CY

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"Unrecognized command" in chimera
by Victoria James 07 Oct '11

07 Oct '11

Hi there, I am having a problem with the chimera command line. Whenever I try and tell it to do anything it says "unrecognised command", e.g. even the most basic "sel" I get prompted with "Unrecognized command: 'sel'" This has only started happening today.. I has a crisis with my computer yesterday and I had to restore all the files from a recent back up which may explain the problem, but I'm unsure how to fix it. I have just tried downloading the program again, but I am still getting the same problem. Is anyone able to help? Thanks in advance. Vicky

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select
by maznar 05 Oct '11

05 Oct '11

Hello, I working about Bam35c virus (emd_1123.map). That virus has a capsid and other things inside. I want used only exterior part (between 315 and 335 amstrons) and discard other parts. How can I select only this external part? Thank you for your help María

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Ribbon Structures From Gaussian Output
by Michael Lodewyk 30 Sep '11

30 Sep '11

Hello, I'm interested in using Chimera to visualize oligopeptide structures computed with Gaussian09 as ribbon structures... that is I'd like to be able to render an alpha helix backbone as a ribbon and then select specific residues/ligands to be rendered as tube or ball & stick models. While I can save or convert the Gaussian output file to a variety of formats, they do not inherently contain the information necessary for such a rendering of the structure, as one would find in a true .pdb file. So my question is... Is Chimera the correct place to start for creating such representations? If so, can you please point me to any documentation that would assist me in doing so? Thank you, Dr. Michael Lodewyk Tantillo Group, UC Davis

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Using addaa at the N-terminus?
by Tosan Omabegho 30 Sep '11

30 Sep '11

Hi, I read in the manual that addaa can be used at the N-terminus. I'm not having any luck doing this. I've been assigning the amino acid to add at the N-term with a lower number, like: addaa cys,5,alpha :6.a The error message says 'Can only add to last residue'. Is there something I may be doing wrong? Thanks, Tosan

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Chimera for Mac 10.7
by Michael Chou 27 Sep '11

27 Sep '11

Hi Chimera Team, Which version of Chimera do you recommend I download in order to use for Mac 10.7? I downloaded chimera-1.5.3-mac.dmg<http://plato.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=mac/ch…>. Although it opens, I cannot use any of the features such as any of the actions or presets. Thank you, Michael

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Protein
by sanabaseer＠sbcglobal.net 27 Sep '11

27 Sep '11

Hello, Please help me with managing the chimera program. I have created an image of a protein, but would like to view the active site complex. How can I highlight that in my image? Thank you, Sana Sent from my U.S. Cellular BlackBerry® smartphone

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ribbon display of circular DNA structures
by jens j birktoft 26 Sep '11

26 Sep '11

Hi Everybody How can I display a circular DNA structure with three helices without a break at the places where the ends meet according to the numbering system. In the real structure there is no break in the covalent structure Best Jens *+++++++++++++++++++++++++++++++++++++++++++++++++++++++* * * *Jens J. Birktoft New York University, Department of Chemistry. **e-mail: jb160(a)nyu.edu <jens.knold(a)gmail.com> **Phone: 212-749-5057 *

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matrices
by Dougherty, Matthew T 26 Sep '11

26 Sep '11

I was doing something with crystallographic point group matrices. Does Chimera allow for improper rotations and inversions? Or does it rectify them as proper rotations? I would like to go from Model 0.0 1 0 0 0 0 1 0 0 0 0 1 0 TO Model 0.0 -1 0 0 0 0 -1 0 0 0 0 -1 0 Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ________________________________________

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importing chimera module question
by Lockwood, Svetlana 22 Sep '11

22 Sep '11

Hi to everybody! I am new to Chimera. I've just installed Chimera and trying to run a python script. I get the import error: no module named chimera. My OS is Win7 and Chimera 1.5.3. I checked my path under enviromental variables and added Chimera folder in there. Still nothing changed. There must be an easy fix to this. Please let me know what could be done. Thanks!

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Re: [Chimera-users] Has the option provided by surfvalues.py script been incorporated into Chimera?
by Tom Goddard 22 Sep '11

22 Sep '11

Hi Boaz, Ok, I added today a "Report value at mouse position" option to the Surface Color dialog. If you are showing electrostatic potential on a surface with that dialog the numbers are reported in the status line as you move the mouse over the surface. It works for all the modes of coloring surfaces (radius, cylinder radius, height, volume data value, volume gradient, ESP value). It will be in tonight's Chimera builds. Tom Boaz Shaanan wrote: > Hi Tom, > > A while ago you wrote the ver useful surfvalues.py script to show > actual potential values while wandering with the mouse over the > surface. I wonder whether it has been incorporated into the Chimera > version by now. I couldn't figure out whether it has. > > Thanks, > > Boaz > /Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > /

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Re: [Chimera-users] SASA calculation in Chimera
by Elaine Meng 21 Sep '11

21 Sep '11

Hi Horacio, Chimera is using MSMS to generate the surface and give surface area values per atom. There is more information and an MSMS reference here: <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfa…> I hope this helps, 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 Sep 21, 2011, at 9:01 AM, Horacio Pérez-Sánchez wrote: > We have developed a fast and accurate new GPU based SASA calculation method. It can bring information about SASA per atom and also grid per atom necessary to graphically render the molecular surface. We are new to Chimera but we would like to know: > > a) where could we find information about the SASA method Chimera uses so we can test with our own method > b) same question for the method Chimera uses to graphically render the molecular surface > > Thanks in advance, > Horacio > >

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Re: [Chimera-users] Atom selection by number ?
by Marek Maly 21 Sep '11

21 Sep '11

Thanks a lot Victor it works ! Best wishes, Marek Dne Wed, 21 Sep 2011 14:47:36 +0200 Victor Muñoz <chewaka.87(a)gmail.com> napsal/-a: > you should try using: > > select @/serialNumber=31 > > Best wishes, > > Victor Muñoz > > > > __________ Informace od ESET NOD32 Antivirus, verze databaze 6481 > (20110921) __________ > > Tuto zpravu proveril ESET NOD32 Antivirus. > > http://www.eset.cz > -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Has the option provided by surfvalues.py script been incorporated into Chimera?
by Boaz Shaanan 21 Sep '11

21 Sep '11

Hi Tom, Here is the plain text version (I keep forgetting that the list has a problem with html formatted messages, but is it always the case? ): A while ago you wrote the very useful surfvalues.py script to show actual potential values while wandering with the mouse over the surface. I wonder whether it has been incorporated into the Chimera version by now. I couldn't figure out whether it has. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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color surface by electrostatic potential from apbs dx file
by matheus froeyen 21 Sep '11

21 Sep '11

Hi I try to show the electrostatic potential calculated by apbs and written to a pot.dx file. This works fine when using the mouse / menus. However I try to do this also using the command line interface because I need to repeat it many times. $ chimera chimera.cmd $ cat chimera.cmd: open prod30.pdb ~ribbon : ~fillring : surface : open pot.dx ~scolor #0 scolor #0 volume #1 cmap rainbow scolor #0 volume #1 cmap -15,red:-5,yellow:0,green:5,cyan:15,blue I don't get an error but the surface is colored by volume data, not by electrostatic potential. Also the popup window "Surface Color" is not updated for the selected colors. In the surface color popup I need to select color surface "MSMS surface" again, change "volume data value" to "electrostatic potential" and then push the button "Color". Then I get what I want, but unfortunately using the mouse again. This should be done by the script too, I guess? I m using the last stable chimera 64 version for unix on redhat. best regards mathy

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Smoothing a trajectory
by Daniel Gurnon 20 Sep '11

20 Sep '11

Hi everyone, For the purpose of making educational content, I'm interested in smoothing out the often jumpy transitions from frame to frame in a MD trajectory. My approach was to write two python scripts (with critical help from Eric of course); one goes through the trajectory and saves pdbs of each desired frame, while the second opens these pdbs and creates a morph, interpolating from one pdb to the next. It seemed like I was almost there, and it looked great when I tried 50 frames.....but Chimera crashed when I tried morphing 200 frames, adding 3 frames of interpolation between each. Is there a better way to add transitions in between (ideally thousands of) frames of an MD trajectory? Thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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segmentation tool
by Jean-Francois Menetret 20 Sep '11

20 Sep '11

Hi, I am using the segmentation tool on a ~15A cryoEM map. I have noticed that the surface of the mrc maps saved from selected areas look pixelated. Any suggestions how to improve the quality of the segmented maps ? Best wishes Jean-François Ménétret

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mailling list hiccup
by Greg Couch 19 Sep '11

19 Sep '11

We had an internal problem with all of our email over the weekend. So if you sent email to chimera-users and it bounced, please resend it. It should work now. -- Greg

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Double coordinates for same residue
by Francesco Pietra 15 Sep '11

15 Sep '11

Hello: Surely a naive question: While beginning to treat a multichain, engineered protein - downloaded from PDB web (1.94 A resolution) - with Chimera, I noticed that many amino acids have such feature as GLU 252 below. Same for many SER, ILE, HIS (two imidazole rings for the same residue number) ATOM 2022 N GLU A 252 15.171 -45.532 45.115 1.00 26.12 N ATOM 2023 CA AGLU A 252 14.023 -44.631 45.214 0.50 26.30 C ATOM 2024 CA BGLU A 252 14.048 -44.592 45.252 0.50 26.30 C ATOM 2025 C GLU A 252 13.983 -43.654 44.050 1.00 25.90 C ATOM 2026 O GLU A 252 12.894 -43.403 43.470 1.00 25.36 O ATOM 2027 CB AGLU A 252 13.974 -43.909 46.559 0.50 26.93 C ATOM 2028 CB BGLU A 252 14.170 -43.759 46.533 0.50 26.77 C ATOM 2029 CG AGLU A 252 13.283 -44.741 47.629 0.50 29.02 C ATOM 2030 CG BGLU A 252 12.874 -43.673 47.313 0.50 29.14 C ATOM 2031 CD AGLU A 252 14.088 -45.948 48.051 0.50 33.10 C ATOM 2032 CD BGLU A 252 12.806 -44.716 48.426 0.50 31.91 C ATOM 2033 OE1AGLU A 252 13.481 -47.014 48.330 0.50 34.82 O ATOM 2034 OE1BGLU A 252 13.394 -44.454 49.504 0.50 31.18 O ATOM 2035 OE2AGLU A 252 15.333 -45.828 48.101 0.50 35.49 O ATOM 2036 OE2BGLU A 252 12.162 -45.782 48.231 0.50 33.14 O ATOM 2037 N GLU A 253 15.141 -43.133 43.683 1.00 24.58 N ATOM 2038 CA GLU A 253 15.225 -42.212 42.559 1.00 25.11 C ATOM 2039 C GLU A 253 14.838 -42.941 41.242 1.00 23.83 C ATOM 2040 O GLU A 253 14.142 -42.383 40.374 1.00 23.54 O ATOM 2041 CB GLU A 253 16.637 -41.603 42.476 1.00 26.18 C ATOM 2042 CG GLU A 253 17.033 -40.722 43.697 1.00 30.81 C ATOM 2043 CD GLU A 253 17.635 -41.491 44.915 1.00 36.16 C ATOM 2044 OE1 GLU A 253 17.540 -42.742 45.032 1.00 35.80 O ATOM 2045 OE2 GLU A 253 18.198 -40.809 45.801 1.00 40.87 O About the protein: SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS MENDOCINA; SOURCE 3 ORGANISM_TAXID: 300; SOURCE 4 GENE: TMOA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: P58KABE; The said residue are not among those not located in the experiment. I am interested in channels, pores and so on in the protein, so that the above issue is of most concern for me. Thanks for aid francesco pietra

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