February 2007 - Chimera-dev - RBVI Mailing Lists

add h
by Virginie Lafont 01 May '09

01 May '09

Hi, I am a new user of chimera and I already have a question. I have an protonated aspartic acid in my protein and I was wondering, is it possible to add hydrogen atom to aspartic acid with chimera? Thanks Virginie

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Camera changes in chimera 1.2348
by Greg Couch 27 Feb '07

27 Feb '07

There used to be three attributes, given in the same units (only ratios where used), eyeSeparation, viewDistance (distance to the screen), and screenWidth (the idea was to scale it to the actual window width, but that was never done). The default values were given in inches: 2.0, 30.0, and and 13.0, respectively. The effective field of view was just under 25 degrees. Now, there is an explicit fieldOfView attribute, because chimera maintains the field of view when resizing the graphics window. Of the original three attributes, only eyeSeparation remains, and it is given in millimeters, and the latter two are replaced with screenDistance and windowWidth. The windowWidth value is automatically computed when the graphics window is resized which in turn adjusts the screenDistance based on the field of view. If the screenDistance is explicitly set, then the field of view angle is recomputed. Defaults for the new values, are 50.8 mm for the eyeSeparation, and 25 degrees for the fieldOfView. - Greg

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New chimera development snapshot available
by Greg Couch 26 Feb '07

26 Feb '07

See <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html> for details (this will be accurate for the next few days, after that read the release notes that are bundled into the chimera snapshot). The snapshot uses NumPy instead of Numeric python, so some third-party extensions may break (eg., parts of EMAN). Other highlights include intial support for PDB 3.0 (remediated PDB) format and built-in POV-Ray raytraced image support. Enjoy, Greg Couch UCSF Computer Graphics Lab

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Re: [chimera-dev] [Chimera-users] programmatic representation
by Eric Pettersen 13 Feb '07

13 Feb '07

Hi Randy, The second argument to Midas.represent() is polymorphic, and if it is a list then is is expected to be a list of atoms. You're giving it a list of models, which results in the 'drawMode' attribute of those models being set (to no effect). Perhaps the polymorphism of the second argument could be improved to handle lists of models (or residues), but right now it doesn't. My suggestion is to use a Selection object based on your list of models, which Midas.represent () can handle, perhaps like so: self.model = ReadSDF.readSDF(tmpfile.name) chimera.openModels.add(self.model) from chimera.selection import ItemizedSelection sel = ItemizedSelection() sel.add(self.model) Midas.represent('cpk', sel) --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu On Feb 12, 2007, at 12:28 PM, Randy Heiland wrote: > I'd like to be able to set the representation (wire, stick, bs, > cpk) of > a model programmatically, in this case, from a plugin. I was > trying the > following, but the newly displayed model would always be displayed in > wire: > > self.model = ReadSDF.readSDF(tmpfile.name) > chimera.openModels.add(self.model) > > #Midas.represent('stick', self.model) > Midas.represent('cpk', self.model) > > Suggestions? > thanks, Randy > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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NumPy in Chimera
by Tom Goddard 06 Feb '07

06 Feb '07

Hi Chimera Extension Writers, If you have written Chimera extensions that use Numeric Python you will need to convert them to instead use NumPy to work with future versions of Chimera. NumPy provides almost all the same routines as Numeric but some function and module names have changed. We are switching Chimera over from Numeric Python to NumPy and will have a Chimera snapshot out in one to three weeks that uses NumPy. We envision having a Chimera production release that uses NumPy in perhaps 3 months. The change was necessary because Numeric is no longer maintained. Numeric will no longer be included with Chimera because dynamic library name space collisions with NumPy occur on the Mac because of certain Chimera compilation options. The conversion of Chimera code was not much trouble, but we had to also convert third party packages that are included with Chimera (PyOpenGL, MMTK, Scientific (for netcdf file reading), MSMS molecular surfaces) and that took some work. Thanks for your patience. Tom

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Chimera-dev February 2007