September 2011 - Chimera-users - RBVI Mailing Lists

help! questions about Join Models
by Joyce Yang 08 Sep '11

08 Sep '11

Hi, I am trying to understand what would exactly happen when join two peptide fragment together. My question is how Chimera manage to avoid any collision of atoms from two fragments. Is there any automatic minimization going on while using this Join Models function? Or it is actually possible to see overlapped coordinates of atoms in space after joining two fragments. Thank you very much. Joyce Yang

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color surface based on NMR Order parameters
by lalit.deshmukh＠huskymail.uconn.edu 08 Sep '11

08 Sep '11

Hello, I like the 'surface color ' feature in Chimera. I think, right now, the surface can be colored by radius, height, volume data and so on.. Is it also possible to color the surface based upon the NMR order parameters or intensity ratios (it will be an Excel file containing just two columns: residue numbers and the respective parameter values)? Or this can be done in some other way? Thanks in advance, Regards, Lalit Deshmukh, University of Connecticut Storrs, CT 06269

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Chimera daily-builds: session support for Animate extension
by Darren Weber 07 Sep '11

07 Sep '11

Hi, There is a recent addition to daily-builds to create a scene called 'session'. It can be seen in the Utilities > Animation dialog. The purpose of this scene is to enable easy, quick return to the saved session state after making a few changes, without reloading the session again. There are two potential problems with this new addition: 1. Some of the saved session data or properties may not be supported by the scene facility, yet. Elaine recently sent me an example session that is not yet supported by the scene facility; it contains a 'selection set' that raises an exception in the scene code. Similar problems may arise with other data models or properties. 2. Assuming everything in a session is supported by the scene facility, the 'session' scene should work. That is, it will work only while all the data that it refers to (e.g., models) are present. If changes result in removing any model data that is within the 'session' scene, the scene will contain 'orphaned' references and it will work only on the remaining model data (if any). When data is removed (closed), the scene facility will issue a prompt (warning) about how it will impact the functionality of the scene(s). This new feature to save/restore sessions is experimental in the daily-builds. For anyone using a daily-build for any mission-critical work, it may be handy to have a work around for the above problems. Try making the following changes to $CHIMERA_INSTALL_PATH/share/Animate/Session.py: 1. Comment out line 51 ("Animate.scenes.append('session')") and type 'pass' beneath it (using the same tabbed indentation). This will only disable the creation of a 'session' scene after restoring any session. All other session support remains enabled for scenes. 2. To completely disable all session support in the Animate extension, comment out all the statements that start with "chimera.triggers.addHandler". 3. If you have no need for anything in the Animate extension, completely remove it by deleting all of the content in $CHIMERA_INSTALL_PATH/share/Animate -- Darren -- Darren L. Weber, Ph.D. Programmer/Analyst on Chimera Development Team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco Mission Bay Campus (MC 2240), Genentech Hall (Room N453) 600 16th Street, San Francisco, CA 94158-2517 dweber[at]cgl.ucsf.edu, (415) 488-5439 (google voice) http://www.cgl.ucsf.edu/chimera/

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Re: [Chimera-users] inter-atomic distances do not show in session after daily build upgrade
by Elaine Meng 07 Sep '11

07 Sep '11

Hi Boaz, Generally it is better to use "Help... Report a Bug" and attach the session so that we have the data, but in this case you don't need to do it -- I just reproduced the problem in my own little test session with one distance. I will report the bug and put you on the CC list. I almost always use daily builds too, but since they aren't tested, occasionally some bug will prevent you from doing what you want or need to do. Sometimes I save more than one daily build. Otherwise, I'm hoping you will be able to use the production release (version 1.5.3) until this is sorted out. If you saved the session in a newer version, however, I understand that may not work. I will put the bug at a high priority. Sorry about that, 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 3, 2011, at 11:53 AM, Boaz Shaanan wrote: > Hi, > I upgraded to the latest daily build and restored a session that had quite a few distances drawn. The dashed lines don't show while the table of distances is still there. Before the upgrade the session was restored several times and always showed the distances fine. Is there a way to resuscitate the display of distances? I sure hope so. > Cheers, > Boaz

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swapna: preserve option
by Bala subramanian 07 Sep '11

07 Sep '11

Friends, 1) I used swapna command with preserve true option but chimera complains it as mangled specifier. The preserve option is denoted in online documentation http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html 2) Just for a try i downloaded the 1VT7.pdb and changed the Guanine (first residue in chain A) to Adenine: swapna A :1.A but i found that added A is rotated. I mean the plane of A is not matching with that G (originally present in the structure). I am not sure if the preserve option is working. To be precise, i want added base to have the same plane as the original one. Thanks, Bala

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Cocoa-Togl
by Alexander Agathos 06 Sep '11

06 Sep '11

Hi, I have seen a patch concerning compiling Togl (a software component of Chimera) in Cocoa based TCL/TK http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/foreign/Togl/togl-coco… The problem is that I can't compile it because of the function in the patch : WindowRef r = TkMacOSXDrawableWindowRef(d); The function TkMacOSXDrawableWindowRef does not exist anymore. Is it possible to guide me on what I need to do? Cheers, Alexander.

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play movie forward then backward - script command?
by Gesa Volkers 01 Sep '11

01 Sep '11

Dear Chimera-Programmers, I like to create a movie in chimera by using a txt script and have some questions. I saw that it is possible to check the box "play forward then backward" in the movie recorder but it does not work when I check the box and then run my script to create the movie (maybe this is not suprising..). How can I include this command into my script commands? Another question. If I use the supersampling command, is it right to use the command as follows: movie record fformat png supersample 4 OR movie record fformat png supersample 4x4 Somehow I cannot see a difference in quality if I use the supersample command like this or if I do not use it at all, so I assume that something is wrong. Also the mp4-file size is always the same. And a third question: I liked to upgrade Chimera to the current version (I use 1.5 (build 31025) 2010-07-20). But after the upgrade all my old saved sessions did not work anymore. Is there a solution for this? Because that keeps me from upgrading.. Thank you in advance for your help! I use Chimera a lot and I am always surprised how helpful the tutorials are and how fast the programmers respond to the users. Gesa -- Gesa Volkers Institut für Biochemie, Molekulare Strukturbiologie Felix-Hausdorff-Straße 4 17489 Greifswald Germany +49 (3834)-864392

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Numbering helices sequentially
by George Tzotzos 01 Sep '11

01 Sep '11

I've been looking in the archive for a procedure describing the sequential numbering (and differential colouring, if possible) of protein helices to no avail. I'd appreciate if anyone could suggest a relevant procedure. Thanks in advance George

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fit molecule with Laplacian filtered map
by Noboru I 31 Aug '11

31 Aug '11

Hello, This is my first time trying to apply the Laplacian filter to a cryo-EM map in Chimera before I perform the global search to fit my crystal structure. However, the resulting map looks like the original map blown up into million pieces with positive and negative density showing. I get the same effect even after I "smooth" the map with the Gaussian filter first. Could someone advise me on how I could use this Laplacian filtered map information to better fit my molecule into the original EM map? Thanks for your help in advance. Noboru

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chemdraw addins
by Bill Wuest 31 Aug '11

31 Aug '11

Hi, I am a big fan of your software and would like to use it in greater capacities (primarily for drug discovery). Is there a way to dock molecules (or better yet import chemdraw files) into chimera and then swap those structures in for ligands bound to crystal structures? I would like to model proposed compounds into a binding site of a protein and riboswitch both of which have the ligand bound in the crystal structure. Ideally I would like to import a chemdraw file which could be minimized by chimera and then be able to limit the docking to the ligand binding area and minimize again. That way I can see how the new analog changes the conformation of the protein. Any help would be greatly appreciated! If it would be easier to chat on the phone please feel free to call the number below. Have a great week! -Bill Wuest ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Bill Wuest Assistant Professor of Chemistry Temple University 130 Beury Hall, Office 448 1901 N. 13th St. Philadelphia, PA 19122 Phone: 215-204-7167 Email: wwuest(a)temple.edu

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Chimera-users September 2011