- Chimera-users - RBVI Mailing Lists

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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starting chimera
by Bala subramanian 26 May '09

26 May '09

Friends, I downloaded the latest chimera build and installed it successfully without any error. When i give chimera in command line, i get the following error. But when i start the chimera 1.3 version, it works without any problem. I am using the latest build in Fedora 10. Traceback (most recent call last): File "/usr/local/chimera_new/share/__main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/usr/local/chimera_new/share/chimeraInit.py", line 374, in init tkgui.initializeGUI(exitonquit, debug_opengl) File "CHIMERA/share/chimera/tkgui.py", line 2587, in initializeGUI File "/usr/local/chimera_new/lib/python2.5/site-packages/PIL/__init__.py", line 309, in checkConfig File "/usr/local/chimera_new/lib/python2.5/site-packages/Togl.py", line 27, in __init__ Tkinter.Widget.__init__(self, master, "togl", cnf, kw) File "/usr/local/chimera_new/lib/python2.5/lib-tk/Tkinter.py", line 1930, in __init__ (widgetName, self._w) + extra + self._options(cnf)) _tkinter.TclError: couldn't choose pixel format Couldn't configure togl widget Thanks, Bala

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Chimera API
by christopher lau 26 May '09

26 May '09

Hi, Does anyone have any documentation on the chimera API? I want to familiarize myself more with the commands that can be used in the Chimera IDLE and python scripts. I have looked at the Example tutorials ( http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/) but aside from the commands used in the tutorial I do not know how to perform other actions on the molecule. One of the commands I would like to run is to rotate the molecule ("roll", in the command line) using IDLE commands. Thanks for your help, Chris

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nmrclust additional request
by Austin B. Yongye 22 May '09

22 May '09

Hi chimera-users/developers, Is there a way to save all the structures (not only the representative structures) of all the clusters identified from an ensemble cluster analysis into their respective clusters? The g_cluster tool of gromacs does these, but I don't think it uses Kelley values to determine the optimal number of clusters. Any help will be greatly appreciated. I would like to perform further analyses on each cluster. Thanks, Austin-

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define attribute error
by Roberto Kopke Salinas 22 May '09

22 May '09

Dear All, I am trying to color code a structure according to HetNOE. When I load the attribute list using "Define Attribute" via the "Structure Analysis" menu the program does not automatically open the "Render by Attribute" menu. If I click and open the "Render by Attribute" menu, the program does not show my file in the attributes list for residues. Does anyone have an idea of why this happen? I have pasted my attribute's list below. Thank you, Roberto attribute: teste recipient: residues :377.000000 0.842818 :378.000000 1.273292 :379.000000 0.763398 :384.000000 0.852818 :387.000000 0.999787 :388.000000 0.572572 :389.000000 1.016109 :393.000000 0.950908 :397.000000 0.761818 :399.000000 0.712411 :402.000000 0.388721 :403.000000 0.495060 :408.000000 0.460664 :411.000000 0.973597 :412.000000 1.036187

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