- Chimera-users - RBVI Mailing Lists

.transparency in bild format
by Keren Lasker 05 Nov '11

05 Nov '11

hello: I am trying to use the transparency option in the bild format. it seems that: .transparency 0.3 .sphere 0 0 0 10 results in a sphere however .color 1 0 0 .transparency 0.3 .sphere 0 0 0 10 results in a black image, it only works if transparency is set to 0. any suggestions what i am doing wrong? thanks, keren.

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Adding sequences to an alignment
by Tom Goddard 02 Nov '11

02 Nov '11

Hi David, Here's the documentation on adding sequences to an alignment in Chimera http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu… It says it uses the Needleman-Wunsch algorithm with parameters you specify unless you have the "Simply append..." option enabled in which case it puts the sequence at the bottom with no gaps if the sequence has exactly the same length as the existing alignment. I guess you don't have Simply Append enabled. Probably Needleman-Wunsch is simply failing to align your new sequence to the existing alignment so it ends up putting it to the right of the existing alignment my inserting a huge gap at the beginning. How similar is the sequence you are trying to add to the alignment sequences? I'm not the Chimera expert on this topic (Eric Pettersen and Elaine Meng are) so I've posted to the Chimera mailing list so they can give you a better answer. Tom > Hi Tom, > My name is David and I'm a postdoc in Jack Johnson lab at Scripps. I'm writing as I've a question concerning the use of Chimera. > I've superimposed two structures in Chimera and generated a structure-based sequence alignement. I have two set of sequences (2 families) with a group associated with one of the two structures (and thus its sequence) and the other group being linked to the second structure. > I tried to extend the structure based sequence-alignement by adding new sequences and adding the first 2 sequences exactly did that i wanted: aligning them to the corresponding reference whose structure is displayed. > However when I add the other group of sequence, it doesn't result in aligning to the other sequence and instead add it after the overall alignment. > I'm sure that I'm missing something obvious, could you please help me sorting that out? > Thanks a lot > Best wishes > David > > David Veesler > Research Associate > The structural Virology lab - Johnson's lab > Department of Molecular Biology > The Scripps Research Institute > 10550, N. Torrey Pines Road > La Jolla, California 92037, USA > > >

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Fwd: sphere viz in Chimera
by Elaine Meng 02 Nov '11

02 Nov '11

Begin forwarded message: From: Elaine Meng <meng(a)cgl.ucsf.edu> Date: January 8, 2008 10:09:06 AM PST To: Adam C Marko <adam.marko(a)ucsf.edu> Cc: Terry Lang <terry(a)lego.berkeley.edu>, sbrozell(a)scripps.edu, Eric Pettersen <pett(a)cgl.ucsf.edu>, Elaine Meng <meng(a)cgl.ucsf.edu> Subject: sphere viz in Chimera Hello, You guys will probably think I'm a nutjob (or prior suspicions may be confirmed), but Adam got me started thinking about how to improve sphere visualization in Chimera, and I wrote a short program akin to showsphere but that takes advantage of features in Chimera (attached at bottom - feel free to use, alter, redistribute, or ignore completely - I spot-checked the output but it's still caveat emptor). The old program showsphere was written in the time of Midas and shows the radii with a dot molecular surface. If you just show the PDB file with the sphere representation in Chimera, that doesn't include the radius information but just uses some default for carbon since the spheres are written as C atoms. The dot surface cannot be used for volume calculations in Chimera. Showsphere also made a separate file for each cluster. Chimera can show solid spheres, and an attribute assignment file can be used to set the radii from the SPHGEN output. Another difference from Midas is that you can read in multiple models from a single PDB file which are then separately displayable and specifiable. It was Adam's idea to take advantage of the controls in the Model Panel. So this new little program puts all the clusters (above a user-specified minimum size) into a single PDB file and creates an attribute assignment file for setting sphere radii in Chimera. The volume enclosed by a "molecular" surface around the cluster can be computed in Chimera. -- Example (using rec.sph, the SPHGEN output from the DOCK6 tutorial http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_… ): f77 chimerasphere.f -o csphere guanine.24% csphere enter name of sphere file: rec.sph rec.sph minimum size to include? 35 35 enter name of output PDB: recspheres.pdb recspheres.pdb enter name of radius assignment file: recspheres.rad recspheres.rad cluster # 1 contains 158 spheres cluster # 2 contains 80 spheres cluster # 3 contains 50 spheres cluster # 4 contains 46 spheres cluster # 5 contains 38 spheres -- then I started Chimera and used the following commands before saving screenshot below: open rec_noH.pdb (also from DOCK6 tutorial) open recspheres.pdb defattr recspheres.rad (to browse to this file instead, use "defattr browse" or Tools... Structure Analysis... Define Attribute. This step generates message "No attributes usable by Render dialog were defined" but that is nothing to worry about; just means "radius" is one of the attributes suppressed from appearing there) rep sphere #1 rainbow models #1 color purple #0 set bg_color white -- screenshot with Model Panel (Favorites... Model Panel) -- note you can toggle display of clusters individually using the Model Panel I originally had the program ask for a model number into which the sphere PDB file would be read, because the attribute assignment file must specify each sphere. For example, if you specified 2, you would have to "open 2 recspheres.pdb" and the assignment file would include specifications like #2.5:1017.het@c The current version doesn't ask and just uses specs like #.5:1017.het@c for which there is a [remote] possibility of matching something other than the sphere, but nonetheless it could happen. Lines for the alternative behavior are still in the file, just commented out. Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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docking sphere visualization
by Trent E. Balius 02 Nov '11

02 Nov '11

Dear Chimera-user list, I believe, currently, Chimera can not visualize docking spheres (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#OrientingtheLigand) files directly, in order to do so, we need to create a pdb file of the spheres and then visualize them. It would be vary helpful for DOCK users if we could visualizes spheres directly from the .sph files produced by sphgen (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Sphgen) or sphgen_cpp. Radius and color information could then also be displayed. This might be a helpful new feature to be included in a future release of Chimera. Thank you, Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/

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MD plotting
by Eric Pettersen 01 Nov '11

01 Nov '11

Hi all, For any of you using Chimera's MD Movie for trajectory playback, I just added the ability to plot atomic distances, angles, and dihedrals for your trajectory. You can click (or drag) on the plot to go to the corresponding frame. You create a plot by using the "Plot" submenu in MD Movie's Analysis menu. Most of the functionality is available in the current daily build, but tomorrow's build will have a couple of additional features: dumping plot values to a file, and showing the numeric value of the plot for the current frame in the list of plots (the value is blanked during playback since updating it slows down playback too much). Feedback welcome. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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alpha helix representation problem
by larif sofiene 29 Oct '11

29 Oct '11

greeting after a MD simulation of an in silico induced mutation A80P (located in an alpha helix) in a monomeric protein i get this strange alpha helix (a wire represented helix) http://imageshack.us/photo/my-images/573/alphahelix.jpg/ is it the induced mutation that break down the alpha 3 helix and disturb orientation of the helix axis or a problem with chimera not recognizing the helix (in sequence tool the helix is no more color filled as alpha helix after inducing mutation) thank you for this piece of art which is CHIMERA :)

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managing CONECT table
by Francesco Pietra 27 Oct '11

27 Oct '11

Hello: In preparing a model comprising various fragments I would like to suppress from the PDB CONECT table two connections to the central transition metal. I wonder whether there are rules for such manipulations. Chimera detects (as a bond) only one of these two connections. thanks francesco pietra

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Re: [Chimera-users] periodic box visualization
by Eric Pettersen 26 Oct '11

26 Oct '11

On Oct 26, 2011, at 4:52 AM, Giovanni Pavan wrote: > 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. Hi Giovanni, I'm sorry but neither of these is currently possible in Chimera. You'll have to use another visualization program (VMD?) if you need these capabilities. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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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 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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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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Chimera movie recorder
by Camilla 14 Sep '11

14 Sep '11

Hi, My name is Camilla and I'm an undergrad student at UNC-CH. I've been using Chimera to create models of fibrinogen polymerization. I discovered that I could make movies of my models to be able to see them from all views. However, my videos are very choppy and since I rotate the model by mouse, the movies are very poorly made. Is there a specific command I could use where I can get the model to rotate 360 degrees by itself to make this movie more smooth and to be able to still see the model all the way around one axis? Thank you, Camilla

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