April 2007 - Chimera-dev - RBVI Mailing Lists

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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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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 07 Apr '07

07 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 02 Apr '07

02 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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Chimera-dev April 2007