- Chimera-users - RBVI Mailing Lists

volume visualization
by Enrico Malito 24 Jan '08

24 Jan '08

Hello, I am trying to visualize a map as Volume (ccp4 format map calculated with VOIDOO in NEWZD then converted with MAPMAN) and somehow the map in chimera results shifted with respect to the corresponding pdb model (in a completely different place). If I open same pdb and map file in other visualization programs they are actual in the right position (map into the cavity of the enzyme). I'm opening the map from the Volume Viewer-->File-->Open map Am I doing something wrong? Thanks, EM -- Enrico Malito Ben-May Department for Cancer Research Center for Integrative Science, W423J The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637 Tel: 773-702-4608 Fax: 773-702-6260 http://home.uchicago.edu/~emalito

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Save a transformed density map
by Keren Lasker 24 Jan '08

24 Jan '08

hello, How can I save a transformed map after using the fit map2map option? The "save map" option saves it in its original transformation. thank you, Keren.

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Chimera batch surface exporter
by Trent Grover 24 Jan '08

24 Jan '08

Hi Everyone, I'm pretty new to Chimera, but I'm working on an animation project that requires quite a few proteins and molecules. To speed up the process, I'd like to create a batch converter/exporter script to do the following: Open a PDB file Generate a multiscale model at a specified resolution Export the model out as a VRML or OBJ file I think I can do this using a Chimera command file, but I was hoping someone could point me in the right direction for some of the relevant command line syntax. Is it possible to control the multiscale model tool via command line (I know I can launch the dialog, but can I change the parameters and execute)? Is there a reference somewhere for the command line parameters for the multiscale models tool? What is the command line export command? Where can I find an OBJ exporter (there are references to it in the mailing list archive)? Any help would be greatly appreciated. Thanks, Trent BTW - I have a suggestion for improvement of Chimera. Add a command history window (or modify the existing one) that echoes out the command line text that is equivalent to any command executed via the Chimera user interface. Maya has this functionality and it is wonderful for anyone who is trying to figure out how to script a process that they know how to execute via the various menus.

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Re: [Chimera-users] Surface representation
by Elaine Meng 24 Jan '08

24 Jan '08

> Hi, > I would like to know if there is a way to build a surface > representation from a pdb file of a dummy atom saxs model in > chimera. The file consist only of CA atoms. I could simulate this > by increasing the vdw radius but the model becomes way to big. > Thanks > James Hi James, You can use Multiscale Models to make a contour surface that encloses the "atoms." The tricky part may be adjusting the contour surface parameters to get the desired smoothness and enclosed total volume. At least in my tests, Chimera did not like the columns in your file after the B-factor column, so I made a version with those removed and opened it with "File... Open" before proceeding. I will send you that file in a separate message. (1) for purposes of comparison to the surface, I displayed the atoms as spheres with the radius 3.75 (this value was given in comments in the file) using the following commands: setattr a radius 3.75 rep sphere You can show the command line with Favorites... Command Line. (2) started Multiscale Models (under Tools... Higher-Order Structure), clicked the "Make models" button near the bottom. This generates the contour surface but hides the spheres. To also show the spheres, Ctrl-click on the surface to select it, and then in the "Style" line of the dialog, choose "Show also.. Spheres". To see spheres inside the surface, make it transparent; set Transparency to some fraction, say 0.3. (3) Then you can fiddle with the contour surface parameters in the Multiscale Models dialog. Many are hidden but can be shown by checking the box next to "..." I got a fairly decent enclosure of the spheres with all default parameters except setting the "Threshold atom density" for "CA only" to 0.0006 instead of the default 0.002. You could also fiddle with the smoothing parameters and resolution if that is not good enough. If you have some idea of what total volume the surface should enclose, that can be evaluated with Measure Volume and Area (under Tools... Volume Data). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Re: [Chimera-users] Chimera-users Digest, Vol 57, Issue 24
by Jonathan Hilmer 22 Jan '08

22 Jan '08

POV-Ray also works extremely well as a distributed job. This site has some basic discussion of some of the distributed POV options: http://columbiegg.com/httpov/?p=why Jonathan > Today's Topics: > > 1. (no subject) (jean-francois menetret) > 2. Re: Flip handedness of map (Tom Goddard) > 3. VRML alpha vs 1-alpha (Nils Becker) > 4. Re: VRML alpha vs 1-alpha (Greg Couch) > > > ------------------------------ > > Message: 4 > Date: Tue, 22 Jan 2008 10:37:54 -0800 (PST) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] VRML alpha vs 1-alpha > To: Nils Becker <nils.becker(a)ens-lyon.fr> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <Pine.OSF.4.63.0801220934340.1761700(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > On Tue, 22 Jan 2008, Nils Becker wrote: > > > Hi, > > > > I found information on the web site that VRML models use > > 1-alpha blending for transparency, and that that looks ugly. > > I agree. > > > > Now I have externally generated VRML files including transparency. > > > > Is there a way to get nice (normal) transparency rendering of these > > models in chimera? > > > > e.g. editing the vrml files, converting them to another format or some > > option inside chimera? > > > > Thanks for any help, cheers, Nils > > The VRML transparency is 1-alpha, because alpha is an opacity value. So > that is just an alternative way of saying that same thing, and is not the > reason it is worse. > > The reason VRML transparency is worse is that there is no sorting within > the VRML shapes, so the blending of transparent objects has to be > drawing-order independent, so VRML uses additive blending. > > The simpliest solution would be to live with chimera's current depiction > and use the Save Image dialog to generate a ray-traced version. The > ray-traced version will be much nicer (and take a lot longer to compute, > try using the POV-Ray 3.7 beta on a multi-core computer to speed things > up). > > The other solution, is to write some Python code and use the _surface > module's Surface_Model and Surface_Group classes. That is, convert each > VRML object into a triangulated surface, a Surface_Group, and put all of > the Surface_Groups into one Surface_Model. All surfaces within one > Surface_Model are sorted so that the transparency is correct for more than > one overlapping surface (unlike the transpareny in chimera between > models that only works for one level of transparency). You can see > examples that use the _surface module in the GraspSurface, IMOD, > Icosahedron, and Intersurf modules (and others) in the CHIMERA/share > directory of your installation. > > If you have any questions about the _surface module, please ask them on > the chimera developers mailing list, chimera-dev(a)cgl.ucsf.edu. > > Greg Couch > UCSF Computer Graphics Lab > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 57, Issue 24 > ********************************************* >

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VRML alpha vs 1-alpha
by Nils Becker 22 Jan '08

22 Jan '08

Hi, I found information on the web site that VRML models use 1-alpha blending for transparency, and that that looks ugly. I agree. Now I have externally generated VRML files including transparency. Is there a way to get nice (normal) transparency rendering of these models in chimera? e.g. editing the vrml files, converting them to another format or some option inside chimera? Thanks for any help, cheers, Nils

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(no subject)
by jean-francois menetret 21 Jan '08

21 Jan '08

In older versions of Chimera, it was possible to change the handedness of a map with a minus sign for the pixel size of the axis. How do you do that in the newer version ? Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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visualizing density map
by francesco zonta 20 Jan '08

20 Jan '08

Good morning. I have some problem in visualizing a ccp4 density map with chimera. I can see only a small slab of the map, but i need to visualize a larger reagion. How can I enlarge the visualized volume? thank you for the help Dr. Francesco Zonta

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Re: [Chimera-users] visualizing density map
by Tom Goddard 18 Jan '08

18 Jan '08

Hi Francesco, Your map contains only the crystal asymmetric unit. Coot is able to replicate that asymmetric unit (using the 4 space group symmetries and unit cell translation symmetries) to show the map for a bigger region of the crystal. http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_6.html#SEC… Chimera is not able to do that replication. Chimera can only display the part of the map present in the file. You might be able to export a map from Coot that covers a larger region but I do not know how. This replication of the crystal asymmetric unit is a nice feature and I'll add it to the list of requested features for Chimera. Tom francesco zonta wrote: > Hi thomas, here is how I can see the map with coot > This is a cubic box of 60 angstrom. [Image deleted] > The problem I have is probably that with chimera I can not see a > bigger volume, but I do not know why. > > Francesco

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VRML rendering options?
by Nils Becker 18 Jan '08

18 Jan '08

Hi, I have been using Chimera for a while and find it great software. Now I am trying to include my own VRML models and show them together with PDB data. I succeeded in opening an externally generated VRML 2.0 file. Since the VRML file contains colored boxes, the standard smooth rendering is not appropriate. Is there a way to influence the rendering style? Also, is there a way to switch on a fixed transparency (alpha value) for the whole VRML model, on a per-model basis? Any help would be appreciated! Cheers, Nils

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