- Chimera-users - RBVI Mailing Lists

surface texture export
by Laura Lynn Gonzalez 09 Oct '12

09 Oct '12

Hi. Is there any way to export Coloumbic colored surfaces as JPG textures when you export geometry (obj, vrml, etc)? Or get the 3D texture data in some other format? I'm trying to import my Coulombic-colored protein into a 3D program. -Laura Lynn

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Re: [Chimera-users] APBS interface in Chimera
by Baker, Nathan 08 Oct '12

08 Oct '12

Hi Boaz -- That was news to me as well; thanks for making me aware of this! Best, -- Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me From: Boaz Shaanan <bshaanan(a)exchange.bgu.ac.il<mailto:bshaanan@exchange.bgu.ac.il>> Date: Monday, October 8, 2012 11:24 AM To: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Cc: Nathan Baker <nathan.baker(a)pnnl.gov<mailto:nathan.baker@pnnl.gov>> Subject: APBS interface in Chimera Hi, Totally due to my negligence I've only just discovered the long sought APBS interface in the daily build (the one I'm using is from 25/9). Well done Chimera and APBS teams! Practical question: I don't see on the APBS pull-down menu where I define the location of the executable (I'm talking about the Windows version right now, soon I'll try the linux version too). Is it clever enough to find it wherever APBS is installed or have I missed something? Cheers, 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<mailto:bshaanan@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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Re: [Chimera-users] using modeller through chimera
by Elaine Meng 08 Oct '12

08 Oct '12

On Oct 8, 2012, at 2:21 AM, Taufiq Rahman wrote: > Just wonder whether in using modeller through Chimera interface, we can use our own alignment file or not. Hi Taufiq, Yes, you can definitely use your own alignment file -- just open it in Chimera. To run Modeller using the Chimera interface, all you need is a sequence alignment of target and template (and if it has additional sequences, that is fine) plus the template structure, both opened in Chimera. There are several ways of obtaining these inputs, outlined here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu…> See the third one, "using a pre-existing target-template sequence alignment" Regards, 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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НА: Chimera --send on MacOS
by Sp 07 Oct '12

07 Oct '12

Отправлено с моего коммуникатора HTC

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Re: [Chimera-users] Chimera-users Digest, Vol 114, Issue 2
by Pu Qian 05 Oct '12

05 Oct '12

Hi, I'm working on a big protein complex with MW ~500 kD. It contains a cave inside of the protein. Now I would like to high light this cave so that I can show the room that is big enough for a quinone molecule to move. Question is: is there a function in Chimera which allows users to produce such cave inside of the protein based on PDB file of the protein. If is, where can I find it and how to use it. It would be a great appreciated if anyone here could give me advices. Thanks. Best regards Dr. Pu Qian Department of Molecular Biology The University of Sheffield Sheffield, S10 2TN UK

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Chimera --send on MacOS
by François Stricher 04 Oct '12

04 Oct '12

Hi all, I want to be able to interact with Chimera from another program, sending commands and all. I tried the chimera --send my_file.com to test it under MacOS 10.7. Each time I do this, it opens a new instance (instead of reusing the previous one) and doesn't process my_file.com at all. When I open my_file.com from inside chimera, it operates the commands inside it without any problem. Any idea? Francois

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Global and per-user preference files?
by mike _ 03 Oct '12

03 Oct '12

I wish to deploy a Chimera installation across multiple machines for multiple users. For obvious reasons the users will not have write permission on the application directory. In this scenario Chimera's default behaviour of regularly checking for updates is unhelpful so I wish to disable it. Having read http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Preferences I assumed I could disable the update checking by putting a suitable preferences file in the application directory and then having users invoke Chimera in such a way that preferences file is found. That works, but generates a warning that the preferences file is read-only (which it is, it's in the application directory) and Chimera seems to only want to use the one preferences file. So the result is that users can't save any preferences. Is there any way to make Chimera read a global preferences file that contains some useful defaults and also allow each user to have their own preferences file? thanks, mike

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Re: [Chimera-users] using modeller through chimera
by Elaine Meng 03 Oct '12

03 Oct '12

Hi Taufiq, As you mentioned, the models will appear automatically in the Chimera main window, and there will be an additional dialog, Modeller results (a list of the homology models and other information). For example, the two bottom figures in the Comparative Modeling tutorial show this dialog: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html> I don't understand what you are clicking... it should not be necessary to click anything. More details about the Modeller results dialog: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modbase.html#modellist> Best, Elaine On Oct 3, 2012, at 6:16 AM, Taufiq Rahman wrote: > Dear Elaine, Many thanks for the reply. It was very helpful and I can now do it. The only fresh problem is: whenever Modeller seems to complete the job (I assume), I can't click on 'modeller results' - its there but clicking on it doesn't open up anything, whilst in the 3d space, I can see the modelled structure as well as the templates. > Any advice? > Regards, > taufiq > > On Oct 3 2012, Elaine Meng wrote: > >> Hi Taufiq, It is probably disabled because you are viewing a single sequence rather than an alignment of 2 or more sequences. In Chimera, there are several ways to get the needed inputs for Modeller, which include the sequence alignment and a structure to use as the template. Some ways are outlined here: >> >> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu…> >> >> Once you have the inputs, you can run Modeller either via web service or via your local installation. If you haven't already, you would also need to obtain a Modeller license key before running (even if you are going to use the web service). >> >> I would also recommend that you get a newer version of Chimera (at least 1.6.2). The Modeller interface is improved in that version compared to older versions. The sequence window menu will then include both "Structure... Modeller (homology)" and "... Modeller (loops/refinement)" instead of a single "...Modeller Tools" entry. >> >> This documentation is for 1.6.2: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> >> >> 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 Oct 2, 2012, at 7:49 AM, Taufiq Rahman wrote: >> >>> Hello, I want to use modeller through Chimera's interface. I have seen the video and read about the way to do it. My problem is my 'modeller tool' option in the structure menu remains disabled. I have installed modeller locally but don't know how to integrate it into chimera. >>> any suggestion? >>> taufiq >> >> > > -- > Taufiq Rahman > MSc(Manchester), PhD (Cantab) > Royal Society University Research Fellow > University of Cambridge > Cambridge > CB2 1PD > UK >

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using modeller through chimera
by Taufiq Rahman 03 Oct '12

03 Oct '12

Hello, I want to use modeller through Chimera's interface. I have seen the video and read about the way to do it. My problem is my 'modeller tool' option in the structure menu remains disabled. I have installed modeller locally but don't know how to integrate it into chimera. any suggestion? taufiq

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crystal structure reconstruction
by rainy908＠yahoo.com 01 Oct '12

01 Oct '12

Hi, I am new to Chimera. I have a PDB of a protein comprising of a loop region that appears to have slight alpha-helical behavior when visualized in Pymol. However, I doubt that this region is actually structured, and that this alpha-helical behavior is actually an artifact from experimental conditions. To double-check the validity of this loop, I was broadly advised that "crystal structure reconstruction" can be performed in Chimera. I suspect this is either the 'molmap' or "Fit in Map" feature? Sincerely, Lili

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Error inizializing OpenGL
by Francesco Pietra 01 Oct '12

01 Oct '12

Hello: Following and upgrading of Debian GNU-Linux i386 testing (= wheezy) of my old PC francesco@deb32:~$ lspci | grep VGA 01:00.0 VGA compatible controller: NVIDIA Corporation NV11DDR [GeForce2 MX200] (rev b2) francesco@deb32:~$ with modern kernel francesco@deb32:~$ uname -r 3.2.0-3-686-pae francesco@deb32:~$ chimera francesco@deb32:~$ chimera --version chimera production version 1.6.1 (build 35849) 2012-03-13 22:24:07 UTC francesco@deb32:~$ does not start anymore: Error inizializing OpenGl. Couldn't configure togl widget. Before I go messing the system, may be I can get advice on where to put the hands. libgotl is not installed, but the same occurs with my GTX-680 amd64 system, where chimera works fine. Thanks francesco pietra

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Re: [Chimera-users] [chimera-dev] The style of Ribbon in alpha 1.7 version
by Elaine Meng 29 Sep '12

29 Sep '12

Hi Cheng, Actually the ribbon shape has not changed, but a bug in the lighting that made the ribbon look rounder than it really was has been fixed. (see release notes "general changes" http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html#general ) You could use Ribbon Style Editor to make something that looks more similar to the old ribbon. I tried making a ribbon style shaped like a football (named "football") and combined that with a ribbon scaling with larger height for helix, sheet, and arrow base (named "fat"). I wasn't very careful drawing the football so you could probably make it better by drawing it more carefully. I attached a file you could use as your preferences file (although you would then lose your own earlier preferences), or you could text-edit to insert all of the lines in the attached file *except* the top and bottom lines into your existing preferences file. Either way, you should save a copy of your existing preferences file first so you don't lose your settings. Or, you could just make a fatter scaling and football-shaped cross section (style) in Ribbon Style Editor yourself, without using the attached file. If you do use the attached file, you could apply everything with commands: ribscale fat ribrepr football Chimera-dev is for programming questions - I'll CC the chimera-users email address since that is more appropriate for this issue, and others on the list may be interested. 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 On Sep 29, 2012, at 3:17 PM, Cheng Wang wrote: > Dear Chimera Team, > Hi. > The ribbon style in 1.6 version is a little round for helix, while it is really flat in 1.7 version. I want to use v1.7 since several commands are really good for movie making eg. format option and transparency. However the ribbon style for helix is not as nice as it in 1.6. I am wondering how could I change the style of ribbon in 1.7 to be the same as in 1.6 since the ribbon style seams the same in the panel for both versions. > Many thanks. > Best, > Cheng

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Specifying colour of surface cap when surface coloured by electrostatic potential
by Ashley Pike 28 Sep '12

28 Sep '12

Hi - Can't find answer to this question in manual. Is it possible to assign a uniform solid colour to a surface cap when the (clipped) surface is coloured by electrostatic potential (using external .dx file)? I know such capping can be done when the surface is coloured by some other attribute but have not found a way to specify in the above case. Any hints gratefully received. Many thanks, Ashley -- Dr. Ashley Pike Membrane Protein Crystallography | Structural Genomics Consortium | University of Oxford

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Silhouette color change
by vamsee 27 Sep '12

27 Sep '12

Hi Elaine, I need to change the silhouette color of individual models and if possible for individual representations (ribbon, surface or atoms). Is there a command line option that I could use? (maybe set?) Thanks in advance Vamsee

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Measuring angles between atoms pairs
by Yasser Almeida Hernandez 26 Sep '12

26 Sep '12

Dear Chimerians... I'm running an analysis about H-bonds geometries in several models. I need to measure the distance of a H-bond and the angle formed with a third atom bonded to one of the H-bond atoms. How could I do that in a python IDLE/script? In a more general way, how could I measure the angle between three atoms linked by a bond o pseudobond? Thanks in advance Yasser -- Yasser Almeida Hernández, BSc. Center of Molecular Immunology (CIM) Tumor Biology Department 216 St.& 15th Ave, Siboney, Playa P.O.Box 16040, Havana 11600 CUBA Phone: (+53-7) 214-3178 almeida(a)cim.sld.cu<mailto:almeida@cim.sld.cu>

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E. coli cells
by Victor Padilla-Sanchez 24 Sep '12

24 Sep '12

Dear UCSF Chimera, Could you tell me where to find chimera maps of E. coli cell(s) ? Or could you send me some maps ? Thank you very much Victor Padilla-Sanchez

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drawing circles
by Bala subramanian 24 Sep '12

24 Sep '12

Friends, I want to draw concentric circles of increasing sizes around the protein. To achieve this, i used the 'define plane' option to draw disk choosing I three reference atoms and drew the disks of increasing sizes and choose two different color for the inner and outer disk. Since the reference atoms are the same. If i change the color of the bigger disk, i get a weird appearance of the inner disk. I dnt know how to resolve this problem. I would like to know if i can do something like making the disk transparent/removing the fill color of the disk. thanks, Bala -- C. Balasubramanian

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"No MMTK name for atom "H" in standard residue "G" "
by Nikolay Igorovich Rodionov 22 Sep '12

22 Sep '12

Hi could someone help me with this error: No MMTK name for atom "H" in standard residue "G" I get this error when running the minimize structure function. Does anyone know a work around or how I can fix the problem? Nikolay Rodionov Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion(a)syr.edu

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Potential Energy Calculations
by Nikolay Igorovich Rodionov 22 Sep '12

22 Sep '12

Hi all, I was wondering the there is a tool in chimera that can find the net interaction potential energy between models, something like Lennard Jones Potential. Specifically, I need to measure the interaction potential between a protein and water in a solvated system. Thanks! Nikolay Rodionov Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion(a)syr.edu

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Calculation of SASA with probe size of 0.8Å
by Amy Davenport 21 Sep '12

21 Sep '12

Hi all, I am trying to calculate the solvent accessible surface area of my protein. I would like to use a probe radius of 0.8Å to do so, but do not see a way to alter the probe size past what the selectable values are in the structools menu. Additionally, I need all atoms to be included, which means hydrogens as well. Any help would be greatly appreciated. Thank you, Amy Davenport Migliori UCSD

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Estimated RMSD after using Modeller feature
by Claudia Fernandes 21 Sep '12

21 Sep '12

I used Modeller function in Chimera to make some comparative models and then used the estimated RMSD function. I used two querys for different modeling jobs. The original query that was similar to the target I choose and a query that has an extra 26 N-terminus aminoacids than the target I choose. Using the same tamplate, shouldn't the estimated RMSD be the same for the original query and the longer query (with the extra Nterminus aminoacids)? As it isn't, how is it being calculated? I found that the calculation was carried out with TSVMod, but I couldn't find anything about how i does it. Any help would be welcome. Regards, Cláudia Fernandes

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Modeller-Chimera interface
by James Valdes 21 Sep '12

21 Sep '12

Hello Chimera, I'm using the Modeller interface via Chimera and I was wondering if the models produced takes into account multiple templates (e.g., selecting all) from a multiple alignment produced by MAFFT (http://mafft.cbrc.jp/alignment/software/) I appreciate any insight you may provide. Cheers, James Jason Valdés, Ph.D.

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arrow heads for pipes and planks
by Evan Kantrowitz 20 Sep '12

20 Sep '12

Hi, Probably a dumb question, but I cannot figure out how to show arrow heads on pipes and planks. I found this info Show arrow on helix and Show arrow on strand (both default true) place arrowheads on the C-terminal ends of secondary structure elements to indicate N→C directionality. These are not on the pipes and planks tool. What is the format on the command line to use this commands I tried Show arrow on helix Show arrow on helix true Thanks Evan ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu<mailto:evan.kantrowitz@bc.edu> Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow<http://www2.bc.edu/~kantrow> Chestnut Hill, MA 02467 -------------------------------------------------------------------

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saving a rotated map
by Filip Van Petegem 20 Sep '12

20 Sep '12

Dear chimera users, I have a problem with saving a cryoEM map after rotating/translating it. I've used the 'fit in map' option to superpose 2 maps (in ccp4 format) This seems to work fine, but when I save the reoriented map (in any of the available formats), and try to open it, it is back to the original position. Is there any way to save the reoriented map file? Best regards, Filip Van Petegem -- Filip Van Petegem, PhD Associate Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpetegem(a)gmail.com http://crg.ubc.ca/VanPetegem/

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solvation box transformed
by Visvaldas K. 20 Sep '12

20 Sep '12

Dear Users, I have some difficulties with reference frames when solvating a protein. The essence of my problem as follows. Chimera solvates a box using _untransformed_ coordinates, but if I try to write out the inpcrd/prmtop, it writes out the _transformed_ coordinates, thus the box planes become no longer parallel to xyz axes, which does not allow to transfer the inpcrd coordinates to another program (NAMD). Of course, I could try a workaround by creating the protein and re-saving it before solvation, and then solvating it while avoiding any mouse movement,or using ambertool cooman line, but maybe there is another solution, or perhaps an "untransformed" button could be implemented in the prmtop tool? Sincerely, Vis

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