January 2013 - Chimera-users - RBVI Mailing Lists

Structure minimization for model with rigid body
by danashah＠post.tau.ac.il 14 Jan '13

14 Jan '13

Hi all, We're interesting in performing a structure minimization for a model, while treating a part of the model as a rigid body. Is "fragment true" the best way to do that, or is there a different option? http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html#fragment Of course the "spec" option will define all the atoms which are not in the rigid body part.... Best, Dana. __ Dana Sachyani Joel Hirsch's Lab Faculty of Life Sciences Tel Aviv University Ramat Aviv, Israel e-mail: danashah(a)post.tau.ac.il

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Re: [Chimera-users] em fit refinement
by Feixia 14 Jan '13

14 Jan '13

Hi Tom, I have a question about multiple fit. Essentially, I have a map of a dimer. For each monomer, I have three domains. I have built models for each of the domain. I tried to fit each individual domain into the map, but found the same domain taking different orientations in different monomer, so I can't achieve 2-fold symmetry. I wonder what would be a sensible approach to fit. Also, what would be a good value to select for 'level' for the map. The map is from negative-staining data with 18A resolution. Thanks a lot! Best, Feixia -- Feixia Chu, Ph.D. Assistant Professor Biochemistry Graduate Program Coordinator Molecular, Cellular & Biomedical Sciences University of New Hampshire Gregg Hall, Rm436 35 Colovos Rd Durham, NH 03824 Tel 603 862 2436

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Is it possible to make an open-book diagram using Chimera?
by Amy Davenport 14 Jan '13

14 Jan '13

Hi - I want to create an open-book diagram showing amino acid interactions present in a buried surface area. I was wondering if it is possible to create these types of diagrams with Chimera without cheating by cutting the protein into two and flipping it. In my experience, it's extremely hard to get things rotated correctly when you do that. Any ideas would be much appreciated. Thank you. Amy Migliori UCSD

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Chimera crashes at launch
by Gökhan Tolun 14 Jan '13

14 Jan '13

Hi, I was running Chimera 1.7s 64bit under Windows 7 64 bit, and all was fine until I started trying it with a 3D monitor. While I was playing with stereo options, Chimera crashed and now it gives me an error at launch and quits, so I cannot run it anymore. I uninstalled it, deleted its preferences folder .chimera from AppData folder, cleaned up chimera occurences from registry and reinstalled the daily version, and it still doesnt work! After launch, the error window shows: --------------------------- Chimera Launcher Error --------------------------- chimera failed abnormally; the exit code was: 1. Use the --debug command line option for the full error message. --------------------------- OK And if I launch it with the debug option, this is what I can see in the terminal (command line): Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics create application loading Pmw creating main window creating menus creating toolbar creating viewer initializing OpenGL initializing preferences initializing dialogs initializing COM initializing extensions Traceback (most recent call last): File "c:\Program Files\Chimera 2013-01-11\share\__main__.py", line 69, in <mod ule> value = chimeraInit.init(sys.argv) File "c:\Program Files\Chimera 2013-01-11\share\chimeraInit.py", line 651, in init extraArgs = tkgui.finalizeGUI() File "c:\Program Files\Chimera 2013-01-11\share\chimera\tkgui.py", line 3623, in finalizeGUI _firstStatus(lastVersion) File "c:\Program Files\Chimera 2013-01-11\share\chimera\tkgui.py", line 3528, in _firstStatus statusline.show_status_line(True) File "c:\Program Files\Chimera 2013-01-11\share\chimera\statusline.py", line 3 98, in show_status_line status.show(show) File "c:\Program Files\Chimera 2013-01-11\share\chimera\statusline.py", line 1 18, in show self.frame.pack(expand=Tkinter.FALSE, side='bottom', fill=Tkinter.X, **kw) File "c:\Program Files\Chimera 2013-01-11\bin\lib\lib-tk\Tkinter.py", line 180 8, in pack_configure + self._options(cnf, kw)) _tkinter.TclError: window ".106614152L.110482120L" isn't packed Return code: 1 Press return or enter to to exit I was planning to get something done this weekend, so Id appreciate any replies. Looking forward to the solution. Thanks and have a nice weekend. Gökhan

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heptamer
by Hossein Lanjanian 14 Jan '13

14 Jan '13

Hi every body. I want to make a heptamer of beta cyclodextrin from its monomer pdb file. is it possible to do it with the chimera software? in other words, can chimera model *heptamer, from, monomer*? -- With The Best H.Lanjanian

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How to install ?
by pythonchemia Gazeta.pl 10 Jan '13

10 Jan '13

Dear Chimera Team ! I intersted in chemistry. I use chimera 1.5 software for personal purposes, non - commercial. Chimera is a very usefull Tool. I like it :). I know Python language a little. I'm beginner programmer. I have Chimera 1.5 with Python IDLE v 2.7 and Windows XP and MinGW. My website is pythonchemia.aq.pl I have some questions: 1 - How to install pDynamo library ? from https://sites.google.com/site/pdynamomodeling/home for Chimera 1.5 automatically or manually ? 2 - How to install OpenBabel library ? from openbabel.org/wiki/Main_Page for Chimera 1.5 automatically or manually ? 3 - How to install Biopython library ? from http://biopython.org/wiki/Main_Page for Chimera 1.5 automatically or manually ? Please help me ! - I wait on answer. Sorry for my english Yours sincerely - Janusz Grabowski

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Showing Binding surface
by Bobo Dang 10 Jan '13

10 Jan '13

Dear Chimera Users, I am trying to use Chimera to show the binding surface between two chains in one Model and measure the area of this binding surface, but I don't know how I can select the bind surface, could anybody give me a hand? the model I am using is 4GLN from PDB. thanks a lot bobo

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Place markers
by Kim Fong 09 Jan '13

09 Jan '13

Hello, Is there an easy way to select a single residue along a chain and center a new marker on that selected residue? Thanks! Kim

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crosslinks
by Trisha Davis 09 Jan '13

09 Jan '13

We would like to show the cross links we recently observed between proteins within a complex. Is there an easy way to specify where to put these 15 cross links? In the past, when we had just a few, we drew them in and positioned them by hand. Trisha Davis

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Color surfaces
by Hernando J Sosa 08 Jan '13

08 Jan '13

Hi I thought there is was way to color density surfaces according to the assigned color of atoms close by (i.e. when there is an a atomic structure fitted into the density), but I can't remember if this was indeed possible or how to do it. Is there a way to do this ? 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 hernando.sosa(a)einstein.yu.edu<mailto:hernando.sosa@einstein.yu.edu>

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Chimera-users January 2013