- Chimera-users - RBVI Mailing Lists

Sending commands via terminal
by cdlau＠ucsd.edu 25 Jun '09

25 Jun '09

Hi, I was wondering if there was a simple way to send commands (such as "open 1zik" or "preset apply int 2" ) to an already running instance of chimera. I want to be able to send this command using 1 line of command. This means that "--start ReadStdin" would not work because it allows commands to be sent indefinitely. Potentially I could write the commands in a python script and use the --send command, however I would like to avoid this if I just want to send a single command to chimera. Thanks for your help, Chris Lau

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high quality pictures for publication
by Fabian Glaser 25 Jun '09

25 Jun '09

Hi all, I am trying to produce high quality figures for publication with chimera, and despite I am working some time with it, I am not quite satisfied with the result I get. I don't know if I can send figures to this list, just as example I send these two. They are fine, but they are not gorgeus as I would like. I don't know they are produced with and without the pov-ray in linux, with 300 dpi, etc. Could somebody try to help me how to improve them? Thanks a lot in advance, Fabian -- Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL Web: http://bku.technion.ac.il Email: fglaser(a)tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396

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Re: [Chimera-users] Surface Creation
by Eric Pettersen 23 Jun '09

23 Jun '09

On Jun 23, 2009, at 2:25 PM, Thiruvarangan Ramaraj wrote: > Hi, > > I tried to create two surfaces, one for the Antibody and one for the > Antigen for an Antibody-Antigen complex (1A14.pdb). I am able to > create two surfaces as two models in one session. But when I try to > save this session it gives me an warning > "Cannot save surfaces without associated structure. > Surface will not be saved." This happens when you close the structure that a surface is based on. Sessions don't store vertex/triangle information for surfaces (which would be voluminous) but instead just the parameters that were used to generate the surface -- and the surface is regenerated when the session is restored. But if the underlying structure is gone then that won't work. > Then when I try to open the saved session there is only surface that > I could see. > > Is there any way that I could have both surfaces saved in one session. > > Any help would be greatly appreciated. Well, obviously one approach is to not close the underlying structure. FYI, you can get separate surfaces on the antigen/antibody without using multiple copies of the structure. You need to get the antigen and antibody into separate "surface categories" (as described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/msms.html ). Here is a sequence of commands (Favorites->Command Line) that gets the antigen (chain N) into its own surface category named "antigen" and then surfaces both the antigen and antibody: surfcat antigen :.n; surf antigen; surf --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Saving image and rendering
by Ibrahim Moustafa 23 Jun '09

23 Jun '09

Dear Chimera team, Recently, I have some trouble saving images with POV-RAY option ³true². The process of rendering is too slow (both on the mac and windows version). To give the feeling of how slow: rendering an image with 1700 lines takes 7 hrs (with quality 9 in pov-ray options) and 2 hrs (quality 5). I used to get the images rendered much faster than that (with older versions; however, I¹m not exactly sure of when I started to see such a slow rendering behavior). There is another related problem but only with the windows version: If I want to save an image, with depth cue, using the fast mode (POV-RAY false), the image output lacks any depth used in the model, with poor quality and darker than it should be. Somehow, the camera orientation is messed. In addition, the depth cue will be no longer available for the rest of the session (I have to restart over again). To get the depth cue I want, I need to turn the POV-RAY option ³true²....but then too slow to create a good figure. I¹d appreciate any comment or explanation from Chimera people; and what is the best way to overcome this problem? P.S. I have the PPC version for the MAC running OSX 10.4; the PC running Windows XP. Many thanks in advance for your help. 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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New surface coloring command
by Thomas Goddard 22 Jun '09

22 Jun '09

I added a Chimera command "scolor" that can color surfaces radially or according to volume data values such as electrostatic potential. This command is the equivalent of the Surface Color dialog. A few examples: scolor #0 geometry cylindrical colors the surface by distance from a cylinder axis (default z-axis) with default coloring red-white-blue ranging from minimum to maximum surface radius. scolor #0 geom radial cmap 100,gray:150,blue:200,purple colors radially with colors gray,blue,purple at radii of 100,150,200. scolor #0 volume #1 cmap -10,red:0,white:10,blue colors surface #0 using volume data #1 with colors red,white,blue for volume data values -10,0,10. Here's a summary of the full command syntax. Detailed documentation will be available in the manual before the next Chimera release. scolor <surfaceSpec> [volume <vspec>] [gradient <vspec>] [geometry radial|cylindrical|height] [color <color>] [center <x,y,z>|<atomspec>] [axis x|y|z|<x,y,z>|<atomspec,atomspec>] [coordinateSystem <modelid>] [cmap <v,color>:<v,color>:...|rainbow|gray|redblue|cyanmaroon] [cmapRange <min,max>|full] [reverseColors true|false] [colorOutsideVolume <color>] [autoUpdate true|false] [capOnly true|false] [perPixel true|false] Tom

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Getting Delphi
by Yasser Almeida Hernandez 22 Jun '09

22 Jun '09

Hi all... Where can i download the Delphi executable to run in Chimera...? Thanks ---------------------------------------------------------------- Correo FENHI

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Electrostatics
by Gawronski, Alexander 20 Jun '09

20 Jun '09

Hello, I'm a student at Carleton University and I need to create meshes with electrostatic coloring for all the proteins in the pdb. I need a way of automating this process with scripts but I can't figure out how. Is this possible to do this through command line? How do I call chimera commands from a script? Any help would be greatly appreciated! Thanks, Alex Gawronski

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Re: [Chimera-users] 3D mouse - connexion
by Nils Becker 18 Jun '09

18 Jun '09

Hi Thomas, I'm also using it (recently, on a daily basis, on Mac OS X). It works very nicely, and it's cheap. Also, try the keyboard shortcuts na, nz etc... cheers, Nils

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3D mouse - connexion
by Thomas C. Marlovits 18 Jun '09

18 Jun '09

Hi, the Chimera documentation indicates that the 3D mouse from Connexion (Space navigator) is supported. I have just asked the company, but they didn't know anything about Chimera. I am wondering, whether you have some good experience using it, or whether you have an alternative mouse model that would work nicely together with Chimera. Tx -Thomas Here is the link at your documentation site: > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#otherinput ------------------------------------------------------------------------------- Thomas C. Marlovits, PhD, M.A.S. Research Group Leader IMP-IMBA Research Center - Research Institute of Molecular Pathology (IMP) - Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA) Dr. Bohr-Gasse 3 Room IMBA/6.02 A-1030 Vienna Austria, Europe fone: (++43-1) 79044-4630 fax: (++43-1) 79044-4401 email: marlovits(a)imp.univie.ac.at

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controling multiscale models from command script
by Marhoefer, R (Richard) 18 Jun '09

18 Jun '09

Dear Chimera Users, for the production of a movie file I like to control some attributes of a multiscale model e.g. the style and the surface transparency through a Chimera command file. Unfortunately I couldn't find many commands allowing to do so in the documentation. How could that be done? Kind regards, Richard Dr. Richard Marhoefer Senior Scientist BioChemInformatics Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: richard.marhoefer(a)sp.intervet.com Phone: +49 (6130) 948 204 Fax: +49 (6130) 948 517 Mobile: +49 175 723 081 4 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. --------------------------------------

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Minimize and solvate with a zinc ion
by Dr. Jean-Didier Maréchal 12 Jun '09

12 Jun '09

Dear all, I want to solvate then minimize (few steps) a structure with a zinc (Zn2+) ion. >From what I saw in the manual, zinc parameters are available in the actual version of the amber force field in chimera. However, I am stuck with troubles. When I solvate I have the following message: Could not determine charges for pre-existing solvent from added solvent for: Zn Zn What do I do wrong? All the best, JD *************************************************** Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es

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Morphing Code Request!
by Eric J. Choi 11 Jun '09

11 Jun '09

Hello, chimera-users, Hi, my name is Eric Choi and currently I am interning at the Ren Lab at mission bay for Dr. Ren. For one of my assignments, I was to make a video of a conformation change of PPAR-GAMMA, from open to closed structure with the addition of a ligand. Upon trying to make this happen, I realized that I need the morphing python code(I believe it is) to be able to complete this step. This is what the movie making tutorial told me in the part "Ligand Flying into Unbound Conformation". If I could get the command to make the morph(python code) that would be great. Thank you! -Eric Choi

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map saving
by Jean-Paul Armache 10 Jun '09

10 Jun '09

hello, i would like to ask you a question concerning map manipulations. sometimes i need to manually fit a map into another map, but when saving the map in the new position, it doesn't retain the coordinates. it simply overlays with the original, unmoved maps. is there something i need to do in order to save it in the new position afore hand ? best regards, jean-paul armache

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movie making
by Schulz-Gasch, Tanja 09 Jun '09

09 Jun '09

Hi there, I used Chimera so far only for making pictures. Now I am doing the first movie steps. I want to combine features like hide, show, rock,... with the MD Movie module to show a morph between different protein conformations. How can this be done? The movie should start with the display part (using hide, show, rock,...) followed by the morphing. However, when using the MD movie module the morph starts at frame 1. Thanks, Tanja __________________________________________ Dr. Tanja Schulz-Gasch F. Hoffmann-La Roche Ltd Pharmaceuticals Division PRCBLM Bldg. 92/2.10D CH-4070 Basel Switzerland Tel. +41(0)61 68 88309 Fax. +41(0)61 68 86459 http://compchem.bas.roche.com:8080/schulzt2/PICS_DB/index.html <http://compchem.bas.roche.com:8080/schulzt2/PICS_DB/index.html> Email: tanja.schulz-gasch(a)roche.com <mailto:tanja.schulz-gasch@roche.com> "The information transmitted in this message is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you receive this message in error, please contact the sender and delete the material from any computer."

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loading chimera
by Bala subramanian 08 Jun '09

08 Jun '09

Friends, I installed chimera 1.4 ( build 27677) build in Fedora 10. The installation was successful but when i run chimera, chimera opens with the following message. ERROR: ld.so: object 'libGL.so' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object 'libGL.so' from LD_PRELOAD cannot be preloaded: ignored. In addition, when i try to capture a high resolution image (300 dpi), chimera closed itself with following message. X Error of failed request: GLXBadPbuffer Major opcode of failed request: 143 (GLX) Minor opcode of failed request: 28 (X_GLXDestroyPbuffer) Serial number of failed request: 75435 Current serial number in output stream: 75437 Locking assertion failure. Backtrace: #0 /usr/lib/libxcb-xlib.so.0 [0x19e767] #1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_lock+0x2e) [0x19e90e] #2 /usr/lib/libX11.so.6 [0xb690e9] #3 /usr/lib/nvidia/libGL.so.1 [0x6536ffd] Kindly write me what is going wrong. Thanks, Bala

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Segementation Fault
by Kshatresh Dutta Dubey 08 Jun '09

08 Jun '09

Respected Sir, I am using chimera since five months. It was running without any error. But today when i am starting chimera it is giving error like segmentation fault. Kindely help me for this problem. Thanks in advance. Kshatresh Dutta dubey

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Displaying surface residues...
by Yasser Almeida Hernandez 05 Jun '09

05 Jun '09

Hi all... I want to know if its possible display surface residues via python script. The idea is import the chimera module inside the script, and it receive (the script), the pdb file to analyze. The script is to run in a classical bash terminal... Thanks.. ---------------------------------------------------------------- Correo FENHI

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chimera on GM945
by Dmytro Kovalskyy 04 Jun '09

04 Jun '09

Hi there, I experience porblems with chimera running on Lenovo X60t in Linux. graphics: intel GM945 I have two installations on the notebook: WinXP and Linux (ALT Linux 4.1.1). Chimera's benchmark under Windows returns preety nice values (see http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/benchmarks, pre-pre last line, Lenovo ThinkPad X60 Tablet 6363WDP). However under linux I can not get even something reasonable to post Surf - 1 Mesh - 26 Contouring 149 Solid 1 Recoloring 5 Is it natural or due to some bugs in Linux drivers/X/kernel? Thanks in advance Dima -- ----------------------------------------------------- Dmytro Kovalskyy, PhD D.Kovalskyy(a)enamine.net Molecular Modelling Group Leader tel.: +38 044 537 32 18 Enamine ltd. fax : +38 044 537 32 53 23, Matrosova str. 01103 Kiev, Ukraine

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Residues that interact with active site
by Abeer Shokeer 03 Jun '09

03 Jun '09

Hello I have a model structure of my protein and I would like to determine which residues that could take part in active site. Can I do that with Chimera? Thanks for your help Abeer

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Deleting parts of secondary structures
by Anindito Sen 03 Jun '09

03 Jun '09

Dear All I have a Chimera session in which I have 6 sets of PDB files (ribbon representation) showing variability in the structures. However I wish to display only few of the subunits. Questions are: 1. How do I delete undesired subunits from all the chains on the command line 2. How do I select particular residues from specific chains (not all the 6).. Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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ribbon transparency
by hsosa＠aecom.yu.edu 02 Jun '09

02 Jun '09

Hi, Is there a command to control the transparency of a ribbon representation or the whole model ?. I'm trying to fade in an out a molecule (in ribbon + wire atom representation) in movie. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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Python -send command and IDLE
by cdlau＠ucsd.edu 29 May '09

29 May '09

Hi, I have 2 questions: 1. Is it possible to use send python scripts (with arguments) to an already running Chimera instance? I know that it is possible to use to use the --send feature, however I wasn't able to send argument in with my python script (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html) I want to be able to pass arguments to a already running instance of chimera similar to the --script feature (but this feature forces a new instance of chimera to open). 2. Along the same lines as the first question, is it possible to use terminal and python commands to manipulate color, rotation, etc. in place of using the IDLE? Currently I am working on a project to that requires communicating with a computer running Chimera through "ssh"ing into the computer. I want to be able to use terminal commands to do basic manipulations of the molecules from the other machine. Thanks for all your help in advanced, Chris

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Re: [Chimera-users] Identifying surface residues
by Elaine Meng 29 May '09

29 May '09

On May 29, 2009, at 11:34 AM, Soumya Ghosh (Systembiologie) wrote: > Dear Dr. Elaine Meng, > Thanks a lot for your kind help.Your suggestions helped me a lot. I > tried to ask you another question. If I want to see the > Vanderwaal's interaction between the two molecules, is it also > possible with this software? Can you kindly suggest me how I should > proceed further. Also if I want to see different type of bondings > like intramolecular / intermolecular: covalent or ionic or any > sorts is it possible to see with this CHIMERA. > Eagerly waiting for your kind reply, > Thanks with regards, > Soumya Dear Soumya, It is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of to me directly, unless you are including private data. You can use Chimera to show all kinds of interactions, but it may be necessary to take a little time to become familiar with the tools and with Chimera in general. You can use "Help... Search Documentation" to look for topics such as "find interactions". See the tools "FindHBond" (equivalent command "findhbond") and "Find Contacts/Clashes." Both tools are under "Tools... Structure Analysis" in the menu. You can click the "Help" button on each tool to see its manual page. Both tools provide ways to control whether you are looking at intermolecular or intramolecular interactions. These tools are also used in the Structure Analysis and Comparison tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> Of course, covalent bonds are shown as connections in the graphics window. Metal coordination bonds are shown with dashed pseudobonds. FindHBond identifies hydrogen bonds, which could include both polar and charged groups. To only find salt bridges (H-bonds between charged groups), you could either get the total results and filter them yourself, or you can select only charged groups beforehand and then tell FindHBond to only use the selected atoms. More detailed instructions can be found in this previous post: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/ 003602.html> Find Contacts/Clashes finds contacts of all kinds. To only find some subset of those, you could either filter the output, or limit the input, similar to the situation for FindHBond described above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) 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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Supersample
by hsosa＠aecom.yu.edu 27 May '09

27 May '09

When using using supersample > 1 to record a movie the movies are not saved correctly (black or random color images) In the command script below the saved movies are OK if the option supersample 3 is eliminated and wrong if included. reset p1 movie record supersample 3 reset p2 reset p8 10 movie stop movie encode output test2.avi mformat avi I'm I doing something wrong ?. I'm running the daily build version of Chimera (May 25). Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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Request for advice on Protein Structure Alignment
by Elaine Meng 27 May '09

27 May '09

On May 26, 2009, at 8:46 AM, Madhura Rale wrote: > Dear Dr. Meng, > I am a post-doctoral researcher working in the the Lab of Prof. W. > D. Fessner, Technical University of Darmstadt, Germany. We work in > the area of Biocatalysis and I am an organic chemist by training. > > We are currently looking for an online software / tool to compare > the active sites of two proteins whose structures are already known. > Our work focuses mainly on the utility of these protein catalysts > for chemoenzymatic syntheses. > > My query is that, if the structures of these two proteins has > already been determined by XRD, is it possible to align their active > site sequences to highlight the similarities of the substrate > binding sites? Would the tools mentioned on your website (list of > online resources for structure superposition) be useful for this > purpose and if so, would it be possible for you to advice on which > would be the best one and how one could go about it? > Our need is to more or less obtain a pictorial comparison of the two > active sites to emphasise on the substrate specificites and > preferences of both the catalysts. I have no experience in such > determinations and I hope that my query is not too unappropriate. > > Thank you. Hoping to be excused for my ignorance and hoping to hear > from you soon, > With warm regards, > Madhura Rale. Dear Dr. Rale, It is a good question -- Unfortunately, there is no simple answer to what is the best method for comparing known structures or active sites -- it generally depends on the specific structures you are comparing! If the two proteins are rather closely related, it is an "easy" case and probably most of the methods will do a fine job. If they are distantly related, it may be that some methods will work and others will not, and which programs are successful will be different for different input proteins. It also depends what you already know, and what you are trying to prove. If you already know that in structure A, residues 10, 12, and 15 correspond to residues 48, 50, and 52 in structure B, then you would simply use any molecular modeling program to superimpose A and B using just those residues. Or, if you already have a sequence alignment of the two proteins, some programs can use that alignment to superimpose the 3D structures. I would just use Chimera to match specific residues, or use a sequence alignment, or even to guess the sequence alignment and then use that to superimpose the structures. I work with Chimera and familiar with it, and know it can do these things. Chimera is not a web server, but can be downloaded free for noncommercial use (Mac, Windows, Linux): <http://www.cgl.ucsf.edu/chimera/index.html> Discussion of how to superimpose structures in Chimera: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> Structure comparison tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> If you try using Chimera and run into difficulties, you can contact me for more specific help. My "online resources" web page <http://www.cgl.ucsf.edu/home/meng/grpmt/structalign.html > is separate from Chimera and is specifically limited to: (a) Web servers and databases (there are other programs, e.g. Chimera, that you could download and then use on your own computer) (b) comparisons based on overall structures (there is another large set of programs that instead focus on binding or active site patterns) Thus if you are more interested in comparing the active sites and not so much the overall structure, a general molecular modeling program may be more useful than the servers in that page, but if your proteins are an "easy" case, probably any of the above would be fine. The active site methods mentioned above are mostly for finding other proteins with a similar active site starting with your one structure of interest (not superimposing two proteins you already know about), so they are probably not very relevant to your situation. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) 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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