July 2009 - Chimera-users - RBVI Mailing Lists

FindClashes: iterative input feeding
by Anna Feldman-Salit 27 Jul '09

27 Jul '09

Dear Users and Developers, I'm interested in using a FindClashes option for a large set of files. It is about finding clashes between a small ligand and enzyme which are found at different conformational stages (more than 10000 each). How can one do it iteratively? I understand this is a scripting or could it be that such an application already exists? Thanks in advance. Regards, Anna

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Removing buried substructures
by Brian & Lanie Grech 27 Jul '09

27 Jul '09

Hi everyone The EM map I am currently working on contains hidden buried substructures and I want to remove these substructures from the map, leaving only the outer layer. Because the map I am working on is very complex, I am finding it difficult to remove the buried substructures using the Volume-eraser Tool. Consequently, I would greatly appreciate any advice on how to remove the buried substructures, without removing the outer layer. Thanks Brian

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wrl to spider or mrc format
by Pierre-Damien COUREUX 23 Jul '09

23 Jul '09

Hello everyone, I'm trying to use this skeleton hand (http://www.cc.gatech.edu/projects/large_models/hand.html) as a teaching tool in electron microscopy. I'm only able to open the file in the wrl format and I was wondering if there is an easy way in chimera to convert that file into a density spider or mrc format. So I can import it and make projections in spider for example. I tried to find on the web a free procedure to convert that wrl, without any success. If you have a clear protocol about how to do that, that would be great Thank you in advance for your help Pierre-Damien COUREUX

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Re: [Chimera-users] [chimera-dev] small suggestion regarding savepos
by Eric Pettersen 23 Jul '09

23 Jul '09

Hi JD, I think you're right: closing a session should clear saved positions. In tomorrow's build that's what will happen. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jul 22, 2009, at 4:20 AM, Jean Didier Pie Marechal wrote: > Dear all, > > I see that when I close a session, the savepos list continues > containing the poses I defined for my anterior session. May be that > is something you want to have this way, but I was wondering if the > savepos (with an option for example) could list only the poses for > the working session. > > All the best, > JD > > > > > Dr. Jean-Didier Maréchal > Lecturer > Computational Biotechnological Chemistry @ Transmet > Unitat de Química Física > Departament de Química > Universitat Autònoma de Barcelona > Edifici C.n. > 08193 Cerdanyola (Barcelona) > Tel: +34.935814936 > e-mail: JeanDidier.Marechal(a)uab.es > > > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Matlab script for reading volume data
by Thomas Goddard 23 Jul '09

23 Jul '09

Hi Do-Nyun, The matlab script on the MRC file format specification web page at http://ami.scripps.edu/software/mrctools/mrc_specification.php was not written by us. But that appears not to be the script you are referring to since it merely reads MRC grid size and data values and does not read the origin, cell size, or cell angles. The Chimera code that reads an MRC map is in Python and included in the distributions: chimera/share/VolumeData/mrc/mrc_format.py It uses other Chimera modules (Matrix and VolumeData) so it can't be used on its own. Tom -------- Original Message -------- Subject: Re: [Chimera-users] save map as ascii From: Do-Nyun Kim To: Tom Goddard Date: 7/23/09 8:22 AM > Dear Tom, > > It seems Voxel information in Volume Viewer is different from that by reading > .mrc map data. > > For example, > I opened "emd_1080.map" and saved it as "emd_1080.mrc". > > In volume viewer, > Origin index = 50, Voxel size = 2.7, Cell angles = 90. > > But if I use matlab script you linked, > Origin = -1022951423, Cell size = 1132920833, Cell angle = 1119092736 > > Could you let me know how to convert values from .mrc data to those shown in > volume viewer? > > Thank you. > > Best regards, > Do-Nyun Kim. > >> -------- Original Message -------- >> Subject: Re: [Chimera-users] save map as ascii >> From: Do-Nyun Kim >> To: Thomas Goddard >> Date: 7/21/09 7:24 AM >>> Dear Tom, >>> >>> Thank you for your nice reply. >>> Can I get some example code in python? >>> I don't need to write it down as text files, but I want to read values in >>> density map. >>> >>> Thank you for your help. >>> >>> Best regards, >>> Do-Nyun Kim. >>> >>> >>> Quoting Thomas Goddard <goddard(a)cgl.ucsf.edu>: >>> >>>> Hi Do-Nyun, >>>> >>>> Chimera does not write volume data in any ascii file format. >>>> Text formats are much slower to read the files are much larger so >>>> EM maps are almost always in binary. It is not hard to read the >>>> MRC/CCP4 binary formats. Here is the specification. >>>> >>>> http://ami.scripps.edu/software/mrctools/mrc_specification.php >>>> >>>> You can use some Python code in Chimera to dump maps as text files. >>>> If there is a strong reason for doing that let me know and I'll >>>> provide some example code. >>>> >>>> Tom >>>> >>>> >>>> -------- Original Message -------- >>>> Subject: [Chimera-users] save map as ascii >>>> From: Do-Nyun Kim >>>> To: chimera-users(a)cgl.ucsf.edu >>>> Date: 7/20/09 1:33 PM >>>> >>>>> Dear Chimera staff, >>>>> >>>>> I'm trying to get the map density data like voxel coordinates and >>>>> density values >>>>> at each voxel from .map files in EM database. >>>>> >>>>> Is there any way to get these data using Chimera? >>>>> >>>>> Or can I save it as an ascii file such that I can read it? All map >>>>> files seem to >>>>> be saved as binary files. >>>>> >>>>> Thank you for your consideration. >>>>> >>>>> Best regards, >>>>> Do-Nyun Kim. >>>>>

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Finding specific voxels in volume data
by Thomas Goddard 23 Jul '09

23 Jul '09

Hi Do-Nyun, Do you mean you want to find grid indices of volume data points inside a surface? or on (near) a surface? If it is a contour surface the problem is simpler since that just amounts to values above or near the contour level. Chimera doesn't have any capabilities to export lists of volume grid indices so this will require writing some code. It may be quite simple using a Python script in Chimera, but I'd have to know precisely what you need. Export Scene includes surfaces but not values at volume data grid points. The exported file is for graphical rendering -- it does not dump the underlying data. Please direct future questions to chimera-users(a)cgl.ucsf.edu instead of directly to me unless confidential information is included. This will allow others to benefit from the answer. Tom -------- Original Message -------- Subject: Re: [Chimera-users] save map as ascii From: Do-Nyun Kim To: Tom Goddard <goddard(a)cgl.ucsf.edu> Date: 7/23/09 7:37 AM > Dear Tom, > > So, now I can easily read and right maps, but I have one more question. > > When I "Export Scene" the surface mesh from a map, how are coordinates > determined? It seems the density map itself does not have coordinate > information. > What I actually want to know is coordinates of voxels in density map "in > current > scene" such that I can figure out which voxel of the density map contains a > point in the surface mesh. > > Thank you for your help. > > Best regards, > Do-Nyun Kim. > > > Quoting Tom Goddard >> Hi Do-Nyun, >> >> The interpolate.py script on the Chimera Python scripts web page >> >> http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts >> >> shows how to get volume data values interpolated at specific points in >> a volume data set. It uses trilinear interpolation from 8 nearest >> grid points. >> >> More details about the volume data objects are in the Python code >> distributed with Chimera: >> >> chimera/share/VolumeViewer/volume.py >> >> >> Tom

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hydrogen bonds
by Bala subramanian 22 Jul '09

22 Jul '09

Friends, I want to see the hydrogen bond between only side chains & only main chain. 1) I want to know if there is any easy way to do this in chimera 2) What is the default distance and angle used in chimera for calculating the hbond. I see that distance tolerance is 0.4 and angle tolerance is 20. Do these values mean default distance and angle. Thanks, Bala

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mmaker - superposing two structures based on a subset of a chain
by Andrea Rossi 21 Jul '09

21 Jul '09

Dear Chimera Team, I was wondering if it is possible to superpose two structures based on a subset of a chain (a domain for example). I tried the command: mmaker #0:1-100.H #2:1-100.h but Chimera doesn't seem to take into account the residue selection. Superposing according to a subset of a chain is particularly useful when the chain is formed by two or more domains and the domains are connected by a flexible linker (as in the case of antibodies). I can provide more specific examples if needed. Andrea

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save map as ascii
by Do-Nyun Kim 21 Jul '09

21 Jul '09

Dear Chimera staff, I'm trying to get the map density data like voxel coordinates and density values at each voxel from .map files in EM database. Is there any way to get these data using Chimera? Or can I save it as an ascii file such that I can read it? All map files seem to be saved as binary files. Thank you for your consideration. Best regards, Do-Nyun Kim. -- Do-Nyun Kim, Ph.D. Laboratory for Computational Cell Biology & Biophysics Department of Biological Engineering Massachusetts Institute of Technology

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depth cueing
by Gabor Papai 21 Jul '09

21 Jul '09

Dear all, I am using Chimera alpha verion 1.4 (build 28110). Whenever I want to save an image on white background with white (or no color) depth cueing and I push the save as button (with supersample 3x3) the depth cueing changes to black. I can change it back to white, but it happens again when I try to save the image. How can I save image with white depth cueing? Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748 Fax +33-3-88653201 E-mail: papai(a)igbmc.fr

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Chimera-users July 2009