- Chimera-users - RBVI Mailing Lists

Matching RGB color code from Adobe Illustrator
by Ajith Harish 30 Mar '10

30 Mar '10

Hello, I would like to color different regions of a molecule corresponding to RGB colors from Adobe Illustrator. Chimera RGB ranges from 0.000 to 1.000 where as the Illustrator RGB ranges from 0 to 255. Could you please let me know how these two scales are related? Thank you very much, Ajith

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Trouble with thermal ellipsoids
by sherden＠caltech.edu 30 Mar '10

30 Mar '10

I can't seem to get the thermal ellipsoids to work. I have a number of .cif files that are all perfectly good files (have been cif-checked) and all of which I know for a fact have anisotropic data as I can get thermal ellipsoids to display from these files in other programs like Diamond (which we are trying to move away from). But any time I select an atom or group of atoms and use either the "aniso" command or the "Show Thermal Ellipsoids" dialogue box I just get: "No atoms chosen had anisotropic information." This is just not true though, I can open up the .cif files in question and see the anisotropic data listed for the given atoms with my own two eyes. Any thoughts? I am probably doing something immensely stupid, that is usually the case with such situations. --Nat (Nathaniel Sherden) California Institute of Technology Department of Chemistry

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RMSD
by Beale, John 29 Mar '10

29 Mar '10

What is the best way to use Chimera to compute the RMSd value of an MD trajectory snapshot relative to the crystal structure of the protein? Thanks! John M. Beale, Jr., Ph,D. Professor of Medicinal Chemistry and Pharmacognosy St. Louis College of Pharmacy 4588 Parkview Place St. Louis, Missouri 63110 (314)-446-8461 Cell: (314)-315-0409 FAX (314) 446-8460 jbeale(a)stlcop.edu

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zones and residue name/number
by Francesco Pietra 29 Mar '10

29 Mar '10

Hi: I was trying to detect all residues (or atoms) within a given distance from a single-atom ligand in model #0 (PDB file). There are several such single-atom ligand atoms in model #0 (practically invisible in chimera as they are not shown at their relative vdw size), each specified by different residue and atom numbers. I want to carry out the task for each single-atom residue. Therefore I can't use the standard command select #0:single-atom-ligand z(or za)<given.distance because that applies to all those single-atom-ligands. Unless the residue can be specified differently (the residue number in place of residue name did not work), the only way that I found to come out was to set different names for the different single-atom ligands. Is anything better? Secondary question: is there any plan to support psf/dcd format (which I am now using for MD with namd) beyond reading movies? Thanks francesco pietra

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Converting SDF files to Mol2 Format
by Nancy 29 Mar '10

29 Mar '10

Hi Elaine, I need to convert a large number of PubChem SDF files into Mol2 format. When I convert an SDF file into Mol2 format, I add partial charges and run energy minimisation on the molecule, as this is necessary for the program I am inputting the files into. So far, I have only used Chimera in this method to convert individual files. Is there a way to convert a large number of SDF files to Mol2 format at once, and also preserve the filenames? Thanks in advance, Nancy

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Question related to chimera H-bond constraints
by snoze pa 26 Mar '10

26 Mar '10

Dear Chimera Users, I have a question related to number of hydrogen bonds. 1. When I am using the Relax H-bond constraints then chimera is showing 76 H-bonds as shown below figure (h bonds are shown in cyan color) http://img260.imageshack.us/img260/6467/screenshotau.png 2. If I will select the option color H bonds not meeting precise criteria differently, then still it shows 76 H bonds with some bonds that do not meet the criteria in red color http://img690.imageshack.us/img690/5607/screenshot1ks.png In 2, Why the red H bonds are different from 1 though H bonds are relaxed. If it is true then why chimera is showing these bonds in Relax H-bond constraints in 1. 3. However, if I will not choose the option to relax H bonds constraints then it is showing 50 H bonds as shown below http://img153.imageshack.us/img153/3822/screenshot2kr.png Thank you very much for your time and help. S

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Binding Pocket Internal Volume Calculation
by ppwanjari 24 Mar '10

24 Mar '10

Hello Everyone, I want to determine the inside volume of a pocket shaped molecule. Does anyone know how can I do it with Chimera? I am only able to measure volume of pocket-making atoms with Chimera, but not the inside volume. Thanks. Piyush

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Chimera crashes on my mac even after a reinstall
by David Chenoweth 23 Mar '10

23 Mar '10

Hi! I recently downloaded a new version of Chimera (Mac OS X (Cocoa, Intel, 64-bit)MD5: e54f53e4313817e26dbc68450bd5312d) and it's been running great until today. After using the program all day it finally crashed just as I was trying to save a session and I didn't get the crash message. I restarted the program and as soon as I tried to open a file the program crashed. I tried shutting my computer down and this didn't help so I deleted that version of chimera from my computer and downloaded it again. After reinstalling the program I still have the same problem and now I'm a bit stumped! I have a lot of work saved in session files from today and I can't seem to get the program to run at all. I am using a new 15 inch Macbook pro (OSX 10.6.2). Any suggestions? Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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Dimer construction from a monomer generated using Modeller
by akshita kumar 23 Mar '10

23 Mar '10

Dear Members, Using 1T3D as template, we have generated a homology model via Modeller. As the biological unit is a trimeric structure we need to generate trimer of the model too. Therefore we undertook structural alignment of the model and individual template 1T3D chains ("a, b , c"). However in our model the loop region that falls at the interface between two dimers is much longer and as a result the loops between dimer overlap each other. Can anybody please suggest a solution for generating a dimer/trimer from the monomer built using homology modelling. Thanks Akshita

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Re: [Chimera-users] Scripting to write / save multiple models into single pdf file
by Eric Pettersen 23 Mar '10

23 Mar '10

Hmm, it seems that you have the Model Panel set to autostart in your preferences. Now, Chimera probably should ignore autostarting tools when it is in nogui mode, but currently it doesn't. So what you will have to do for now (until we fix this) is to start Chimera normally, turn off the autostart of the Model Panel (and any other graphical tools probably), save the new preferences, and then run your script. If you look in the "Preferences" preference category, it will show the location of the preferences file. You could squirrel away your original preferences file somewhere, make the version with no autostarting, copy that somewhere, and then put your original version back. You would then be able to use the no-autostarting preferences by specifying it's location with the --preferences startup option. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Mar 8, 2010, at 7:32 PM, Sumitro Harjanto wrote: > Hi Eric, > > Thanks for the suggestion. I don’t really script, I usually use a c+ > + code / excel to generate the command (.cmd) files. Should be okay > for the automation for now, if I run into any problem then I will > post it up here again. =] > > Mean while I try running the command “chimera.exe –nogui” in PATH/ > chimera/bin but got the following error message. I followed the > instruction and copy over the debug message (below). any advise? I’m > on a win7 X86 platform btw. > > Thanks, > Sumitro > > ----------------------------------------------------------------------------------------------------- > > Chimera failed abnormally; the exit code was: 1 > Use –debug command line option for the full error message. > > -------------------------------------------------------------------------------------------------- > Cannot execute 'gzip': no automatic decompression of .Z files > Traceback (most recent call last): > File "E:\Chimera\share\__main__.py", line 65, in <module> > value = chimeraInit.init(sys.argv) > File "E:\Chimera\share\chimeraInit.py", line 401, in init > extension.startup(startExtensions) > File "E:\Chimera\share\chimera\extension\base.py", line 1056, in > startup > manager.autostartTools(extNames) > File "E:\Chimera\share\chimera\extension\base.py", line 959, in > autostartTools > > emo.activate() > File "E:\Chimera\share\ModelPanel\ChimeraExtension.py", line 23, > in activate > display(self.module('base').ModelPanel.name) > File "E:\Chimera\share\chimera\dialogs.py", line 77, in display > dialog = find(name, create=1) > File "E:\Chimera\share\chimera\dialogs.py", line 62, in find > return d() > File "E:\Chimera\share\chimera\baseDialog.py", line 523, in __init__ > BaseDialog.__init__(self, master, *args, **kw) > File "E:\Chimera\share\chimera\baseDialog.py", line 244, in __init__ > self.fillInUI(self.__top) > File "E:\Chimera\share\ModelPanel\base.py", line 217, in fillInUI > self._addColumns() > File "E:\Chimera\share\ModelPanel\base.py", line 436, in _addColumns > self._buildTable() > File "E:\Chimera\share\ModelPanel\base.py", line 454, in _buildTable > % len(filter(lambda s: s == 1, self.shownColumns))) > File "E:\Chimera\bin\Lib\lib-tk\Tix.py", line 1306, in __init__ > cnf, kw) > File "E:\Chimera\bin\Lib\lib-tk\Tix.py", line 307, in __init__ > self.tk.call(widgetName, self._w, *extra) > _tkinter.TclError: invalid command name "tixScrolledHList" > Return code: 1 > Press return or enter to to exit >

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