- Chimera-users - RBVI Mailing Lists

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 01 Sep '11

01 Sep '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 01 Sep '11

01 Sep '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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(no subject)
by Fakron, Osama Mohamed 30 Aug '11

30 Aug '11

Hello My name is Osama M.Fakron , I am PhD student in Mechanical &Material School at Washington State University , I am working on reconstruct 3D image from SEM 2D images by EM3D software ,I am using Chimera for viewing my reconstructed images , I need some help in getting 3D position for any point in my reconstructed image , and also your supporting is appreciated. All the best for you Osama

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hardware stereo switching between distal and proximal when rotating
by frederick lee 29 Aug '11

29 Aug '11

dear chimera community, i have experienced this issue for some time now. i don't think this is happening with other software like pymol, dsvisualizer, MOE, etc given the same computer and hardware setup. somehow when viewing in hardware stereo mode (sequential stereo), the model will switch back and forth between proximal and distal views during rotations. is there a particular chimera setting that will prevent such from happening. thanks much. fred

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Entra nella mia rete su LinkedIn
by Chinmaya Joshi tramite LinkedIn 29 Aug '11

29 Aug '11

LinkedIn ------------ Chinmaya Joshi ha chiesto di aggiungerti ai suoi collegamenti su LinkedIn: ------------------------------------------ Vorrei aggiungerti alla mia rete professionale su LinkedIn. Accetta l'invito di Chinmaya Joshi http://www.linkedin.com/e/fihlc9-grxnbthx-1b/s9zCzPfFBIFwqUg8JgtGw69rcczGuT… Visualizza l'invito di Chinmaya Joshi http://www.linkedin.com/e/fihlc9-grxnbthx-1b/s9zCzPfFBIFwqUg8JgtGw69rcczGuT… ------------------------------------------ SAPEVI CHE LinkedIn può trovare le risposte alle tue domande più difficili? Pubblica le domande più impegnative su Risposte di LinkedIn e potrai avvalerti dell'esperienza dei migliori professionisti al mondo. http://www.linkedin.com/e/fihlc9-grxnbthx-1b/ask/inv-23/ -- (c) 2011, LinkedIn Corporation

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Re: [Chimera-users] electron density in Chimera
by Elaine Meng 27 Aug '11

27 Aug '11

On Aug 26, 2011, at 1:24 AM, Stefano Luciano Ciurli wrote: > Hello, > for a paper reporting a new structure, I would like to make a figure with Chimera, but I need a map that can be read. I have an mtz map that can be read with Coot, but I think I need to convert it to a format that Chimera can read. I cannot use the EDS server, because the file has not been released on the PDB. > How do I do that? > Stefano Hi Stefano, I didn't know anything about MTZ format, but found some explanation in the PHENIX mailing list that the program PHENIX can do the conversion: <http://phenix-online.org/pipermail/phenixbb/2011-March/016881.html> >From that message, "it's not a simple file format conversion. In this case MTZ file is supposed to contain Fourier map coefficients, and Xplor formatted file will contain Fourier image of electron density map (typically simply called "electron density map"). So this converson also involves a FT. " The PHENIX developers provide documentation and downloads for Linux and Mac. <http://www.phenix-online.org/version_docs/dev-713/phenix_documentation.html> Here's a list of the density formats that Chimera "knows": <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume> Other Chimera developers or users may know more -- so it's generally better to send Chimera questions to chimera-users(a)cgl.ucsf.edu (which I CC'd here) instead of to me directly. 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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