- Chimera-users - RBVI Mailing Lists

periodic box visualization
by Giovanni Pavan 26 Oct '11

26 Oct '11

Dear all, when a periodic system is visualized into Chimera (e.g., a periodic water box), is it possible to visualize explicitly the borders of the periodic box (defined for instance in the last line of coordinate/restart files in case of AMBER format structures)? Last, is it also possible to see the periodic images of the original box along X, Y & Z axes? How? I thank you in advance for the support and I look forward to receiving any feedback from you. Bye Giovanni Dr. Giovanni Maria Pavan SUPSI - Laboratory of Applied Mathematics and Physics (LaMFI) Centro Galleria 2, Manno 6928, Switzerland. e-mail: giovanni.pavan(a)supsi.ch skype: giovanni_pavan phone: +41 58 666 65 60

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periodic box visualization
by Giovanni Pavan 26 Oct '11

26 Oct '11

Dear all, when a periodic system is visualized into Chimera (e.g., a periodic waterbox), is it possible to visualize explicitly the borders of the periodic box (defined for instance in the last line of coordinate/restart files in case of AMBER format structures)? Last, is it also possible to see the periodic images of the original box along X, Y & Z axes? How? I thank you in advance for the support and I look forward to receiving any feedback from you. Bye Giovanni

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Fwd: Re: Upgrade your video/graphics driver. hirose
by Greg Couch 25 Oct '11

25 Oct '11

Forgot to send reply to the list. -------- Original Message -------- Subject: Re: [Chimera-users] Upgrade your video/graphics driver. hirose Date: Tue, 25 Oct 2011 15:02:04 -0700 From: Greg Couch <gregc(a)cgl.ucsf.edu> To: HIROSE Junzo <hirose(a)fupharm.fukuyama-u.ac.jp> This is a common error with Intel integrated graphics and older Intel graphics drivers. The solution, if your system is new enough, is to go to the system vendor's website support pages and download (and install) the graphics driver update. Sometimes the graphics driver is referred to as a video driver. Good luck, Greg On 10/24/2011 03:14 AM, HIROSE Junzo wrote: > Dear Sir > > Side View doesn't work. I got the following command in Side View. > > > Unable to share graphics data with main window. > Upgrade your video/graphics driver. > > > How can I resolve this problem? > > > Dr. Junzo HIROSE > > > ****************************************** > > Fukuyama Univ. > JAPAN > > TEL 084-936-2111 > Email: hirose(a)fupharm.fukuyama-u.ac.jp > > **************************************** > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Question
by Anna Starus 25 Oct '11

25 Oct '11

Hello, I am having difficulty to depict some bonds as solid lines or some as dashed lines for the bonds that are coordinated to the metal. For some reason when I changed one bond to dashed all of the bonds also change to that. How could I ungroup the coordinating bonds to the metal and be able to make some of them dashed and some solid? I would greatly appreciate the help. Thank you, Anna

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delegate
by Zoe Cournia 24 Oct '11

24 Oct '11

Hello, I am trying to use the "delegate" command from the Midas program in Chimera, but the error message I get is that "delegate is not yet implemented". Is there an available "Extension Mechanism" in chimera? If not, is it possible to get the source code for Midas in order to compile it and use it with delegate? Thanks a lot for any help. Best Zoe -- ------------------------------- Dr. Zoe Cournia Investigator - Lecturer Level Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece zcournia(a)bioacademy.gr Office: +302106597195 Lab: +302106597568 Cell: +306944223123 -------------------------------

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Error: Cannot write preferences file:
by Andrew Voronkov 24 Oct '11

24 Oct '11

Dear Chimera users I have problems with preferences file and actually when I run command line for example I instantle get the message: Cannot write preferences file: C:\Documents and Settings\avoron\Application Data\.chimera\preferences Maybe that is some problem with netowrk rights or security options and setup as far as reinstallation doesn't help. Best regards, Andrew

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Upgrade your video/graphics driver. hirose
by HIROSE Junzo 24 Oct '11

24 Oct '11

Dear Sir Side View doesn’t work. I got the following command in Side View. Unable to share graphics data with main window. Upgrade your video/graphics driver. How can I resolve this problem? Dr. Junzo HIROSE ****************************************** Fukuyama Univ. JAPAN TEL 084-936-2111 Email: hirose(a)fupharm.fukuyama-u.ac.jp ****************************************

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Cavities/Pockets
by George Tzotzos 22 Oct '11

22 Oct '11

I'm wondering if there's a way to work out the relative hydrophobicity of pockets/cavities of related receptors. Fetching CASTp IDs and rendering the surfaces of the cavities gives a crude idea of hydrophobicity of a given cavity. However, I'm looking for something that goes beyond visualisation. Any ideas would be most welcome. Best regards George

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protein sequence editing at sequence level
by frederick lee 21 Oct '11

21 Oct '11

hello chimera users, i know how to add or delete an entire sequence entry, but i can't figure out how to delete a portion of a sequence entry or a set of aligned sequences. currently, i have to go to another program (e.g., jalview) to accomplish that. is there a way to do that within chimera? also when i edit a protein structure (e.g., remove chains) and save the resulting structure, the sequence information of the *original* structure is kept in the pdb file. is there a way to only save sequence info corresponding to the structure actually saved? thanks much in advance. fred (relatively new chimera user)

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sym complains group t parameters
by Joe Ping-Lin Hsiao 21 Oct '11

21 Oct '11

Hi, I found an online post about how to use the sym command to duplicate models. The post is here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-June/006433.html The commands in the post are: open 1ei3 sym #0 group t,5,280 axis 1,0,.4 coord #0 surf true I got an error of "Invalid symmetry group syntax "t,5,280"" from the sym command. The versions that I have are daily build Oct 18 on Mac, and Oct 13 on Windows. Thanks, Joe

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split segmented map
by Gabor PAPAI 21 Oct '11

21 Oct '11

Dear chimera team, I've found the map segmentation tool very useful. However I would like to split the map according to the segments. Is it possible to do that? Thanks in advance! Best regards, Gabor ----------------- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748

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how to run the command line chimera without actually opening the GUI
by nurul 20 Oct '11

20 Oct '11

Hello, I have two structures to superimpose using the match command in chimera. Once the structures are matched, I save the two models in one pdb file. I can then just view this pdb file whenever I want. My question is: can I somehow just do this using the terminal? Meaning the graphic of chimera doesn't launch, but I get the pdb file that has the correct rotation matrix of the two superimposed structures. I don't have much programming experience, and I have no knowledge of calculating rmsd. Would appreciate if someone would pinpoint me where to start. Thanks.

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.prmtop/.dcd combination for movie
by Francesco Pietra 20 Oct '11

20 Oct '11

Hello: I am running parm7 amber files with namd, thus having a .prmtop file and a .dcd file. Is there any possibility of having such a melange treated by movie? thanks francesco pietra

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problem in coloring a selected region
by Manish Manish 20 Oct '11

20 Oct '11

Dear Chimera Developer, I want to select a region in protein molecule and then color. I have open a pdb file 1HA0 (attached), and then select a sequence TQNGGSNACKR (attached image) then color in blue (attached image). But this colors non selected part. I am using ubuntu 11.04 natty, VGA compatible controller: Intel Corporation Core Processor Integrated Graphics Controller (rev 18) Subsystem: Dell Device 0447 Kernel driver in use: i915 Kernel modules: i915 and Chimera 1.5.3 . Regards Manish

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Labelling helices
by George Tzotzos 19 Oct '11

19 Oct '11

I've been looking at the documentation to find a way to number (label) protein helices. Perhaps I didn't use the right keywords so I didn't find anything helpful. What I would like to do is give ascending numbers to individual protein helices starting from the aminoacid terminus onwards. Any suggestions will be greatly appreciated. Regards George

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Display misconfiguration error
by Enrico Morelli 19 Oct '11

19 Oct '11

Dear all, after the update to the latest version of chimera, in some machines I receive the error: Display misconfiguration. Please increase the color quality (24bit color or grater), update your display (graphics) driver, ....... I've a lot of workstation with the same graphis cards (Nvidia Quadro) and the same operating system (ScientificLinux 5). I didn't do anything except upgrade chimera. The previous version works fine on all PCs, and the new one in some PCs give me the display misconfiguration. I checked the PCs where the chimera doesn't works, all has the Nvidia drivers working in 24bit mode and with graphic acceleration enabled. So, I don't know how can solve the problem. Someone can help me? Thanks -- ------------------------------------------------------------------- (o_ (o_ //\ Coltivate Linux che tanto Windows si pianta da solo. (/)_ V_/_ +------------------------------------------------------------------+ | ENRICO MORELLI | email: morelli(a)CERM.UNIFI.IT | | * * * * | phone: +39 055 4574269 | | University of Florence | fax : +39 055 4574253 | | CERM - via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY | +------------------------------------------------------------------+

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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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