- Chimera-dev - RBVI Mailing Lists

Protein to ligand shortest distances?
by khar6039＠mail.usyd.edu.au 21 May '07

21 May '07

Hi all, I'm new to chimera and would like a simple way to zone 5 Angstroms around a ligand and then have chimera tell me what the shortest distances are between these residues and the ligand. Is this possible? Cheers, Kate ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Re: [chimera-dev] Placing Chimera markers
by Thomas Goddard 23 Apr '07

23 Apr '07

Hi Karin, There is no programming documentation for Chimera markers and marker sets. You can place a marker at position p = (x,y,z) using import VolumePath VolumePath.place_marker(p) Its radius and color and which marker set it is placed in and whether it is connected to an already selected marker is determined by settings in the volume path tracer dialog. If you don't want to use tho`se dialog settings you can instead use code like: xyz = (5.2, 1.2, -4.2) rgba = (0,0,1,1) # red, green, blue, opacity in range [0,1] radius = 2.0 mset.place_marker(xyz, rgba, radius) Here mset is a marker set. You can get the current marker set shown in the path tracer dialog using code: from VolumePath import volume_path_dialog d = volume_path_dialog(create = True) mset = d.active_marker_set if mset == None: mset = d.new_marker_set_cb() All of the marker routines are in chimera/share/VolumePath/gui.py chimera/share/VolumePath/markerset.py The markerset.py file defines the Marker_Set, Marker, and Link classes that hold the path data. The marker positions are obtained using mlist = mset.markers() for m in mlist: print m.xyz() Markers need not be connected. If they are connected they need not be in a single path. Three or more links can connect to a single marker. To find the links use: llist = mset.links() for link in llist: m1, m2 = link.marker1, link.marker2 # the two linked markers print m1.id, 'connected to', m2.id Hope this gives you some ideas to start with. Sorry for the poor quality of the path tracer code. Suggestions for improving it are welcome. Tom Karin Gross wrote: > Hi Tom, > > I have some questions concerning the makers and markersets in chimera. > > First of all, is there any programmer documentation for the markers? > > I want the users to be able to place markers directly onto my plane. Is there > any possibility to get the coordinates for each marker and place markers with > specific x-,y-, z- coordinates? > > The next feature I want to offer is, that the user is able to define a > path(connected markers) within a volume and then the plane should follow this > path through the volume. > Therefor I need some infomations about the paths, how they are stored?, can I > get out the path for moving my plane onto it?, etc... > > Thanks for your time > -Karin >

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Building a multimer model
by Benjamin G.S. Horsman 08 Apr '07

08 Apr '07

Hello, My name is Benjamin Horsman and I am a student at the University of Toronto. I have what should be a basic (possibly naive) question regarding protein modelling that I was hoping you might be able to answer for me or point my in the right direction. I have been studying the structure of a bacterial protein complex, trying to understand how it interacts with several known binding partners. The complex is known to be a hexameric homomultimer. Recently the structure of the subunit protein was solved. However, only the monomeric form of the protein was determined, and the corresponding PDB file does not contain coordinates for the multimer (i.e., no BIOMT1, BIOMT2, BIOMT3 matrix values). I would like to assemble a model of the hexameric complex for visual inspection and for some docking studies. What would be the best way to accomplish this? There are several structures in the PDB of hexameric protein complexes composed of subunits with very close structural alignment to my protein of interest, differing in two regions of the protein that are outside of the multimer binding regions. I believe that my protein complex posses very similar or nearly identical geometry to these known complexes. Is there any way to basically insert my protein into this geometry? Can this be done in Chimera? If not, is there any program or web server that allows this to be done? Or are you aware of a better way to get this done? Thank you for your time. Any help is greatly appreciated. Benjamin Horsman

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additional SimpleSession variable to facilitate session merging
by Eric Pettersen 03 Apr '07

03 Apr '07

For what I imagine are the very few people who have written extensions that save their state into sessions and that restore their own models from sessions, you should know that I have added a variable to the SimpleSession module named "modelOffset". During a normal session restore, modelOffset is zero. During a session restore where pre-existing models haven't been closed (i.e. the session is being "merged" with the current models) modelOffset is a positive integer that should be added to restored model IDs (not sub- IDs) to avoid collision with currently-open models. This is explained in further detail in the Programmer's Guide example for sessions: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/ Main_SessionSave.html Let me know if anything is unclear... --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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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 27 Feb '07

27 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 07 Feb '07

07 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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large data structures in conditional blocks makes baby Python cry
by Eric Pettersen 18 Jan '07

18 Jan '07

This is actually applicable to any Python code, but is especially relevant to extensions that save data in Chimera sessions: the Python bytecode compiler has a limitation of a maximum of a 16 bit offset in a jump instruction. This means that you don't want to have 64K worth of characters in a single conditional block of code (i.e. if/else, loops, try/except). Otherwise you will get the somewhat opaque: SystemError: com_backpatch: offset too large So if you have data structures that may be potentially large when written to a session file, try to place their definitions in the session file outside of conditional blocks. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Re: [chimera-dev] [Chimera-users] SDF format
by Eric Pettersen 16 Dec '06

16 Dec '06

On Dec 15, 2006, at 5:45 AM, Randy Heiland wrote: > Eric, > May I ask how you go about developing plugins for Chimera? > Specifically, is > there a trick to *not* having to quit/restart chimera when testing new > changes made to the plugin module? May I ask what IDE you use for > developing your Python code? I'm currently using eclipse, but I'm > always > curious to hear of others' experiences. > > Thanks, Randy Hi Randy, I always go the "restart Chimera" route. Chimera typically starts much faster the second and subsequent times since many of it's shared libraries are already loaded into memory. Supposedly you could use Python's "reload" function to load the new version of your module, though I've personally found that to be a bumpy road (though I haven't really tried it recently). You would definitely want to read the documentation for the reload function to get the most out of it, and would probably want to be aware of the caveats noted here: http://pyunit.sourceforge.net/notes/reloading.html As far as an IDE, I pretty much work in the stone age -- inserting print statements as needed! Perhaps others would have suggestions... --Eric

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