July 2002 - Chimera-dev - RBVI Mailing Lists

Mouse Trigger
by Mike Liang 31 Jul '02

31 Jul '02

Hello! Is there a way to register a trigger for the mouse? I want the user to be able to rotate the molecules all they want, but perform my (slow) computation when their done moving the models. So it'll be nice to have a MouseUp-like handler (or maybe you have an alternative method). Thanks! Mike

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Fwd: cancel vs. close
by Eric Pettersen 31 Jul '02

31 Jul '02

Can we put this on the discussion agenda for the next Chimera meeting? --Eric Begin forwarded message: > From: "David E. Konerding" <dakone(a)uclink.berkeley.edu> > Date: Wed Jul 31, 2002 10:11:47 AM US/Pacific > To: pett(a)cgl.ucsf.edu > Subject: cancel vs. close > > Why do you guys use the button named 'cancel' where it you should be using > 'close'? I think we had this > discussion at a chimera group meeting before. But normally, I think of > "cancel" in the literal sense- cancel > the change I made (not that the Windows desktop uses it to mean that) > rather than "close the dialog window" > (which isn't a cancellation). > > Dave

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request for feature
by David E. Konerding 31 Jul '02

31 Jul '02

Hi, I would like the following feature: I can currently load a pdb file from the command line using: pdb:1oct which is very convenient. Now, I would love to have a feature where I could load a scop PDB file using: scop:d1octc1 I am currently using the following code fragment to load scop PDB files, which are all available on the web: PDBSTYLE_ADDRESS = "http://astral.stanford.edu/pdbstyle-1.59" domainfile = "%s/%s/%s.ent" % (PDBSTYLE_ADDRESS, self.domainName.get()[2:4], self.domainName.get()) print domainfile f = urllib.urlopen(domainfile) pdb = f.read() f.close() t = tempfile.mktemp() f = open(t, "w") f.write(pdb) f.close() mols = chimera.openModels.open(t, type="PDB") A glance at the pdbstyle-1.59 page, http://astral.stanford.edu/pdbstyle-1.59.html also suggests that rather than retrieving by filename, this CGI script will retrieve the PDB file directly, without the need for knowing the directory structure schema: <form method="get" action="pdbstyle.cgi"> <input type=submit value="Retrieve"> the PDB-style file for <b><font size=-1>SCOP</font></b> domain <input type ="text" maxlength=7 size=7 name=id> (i.e. "d1dlwa_") I'm fairly confident the url won't change; I can check with the astral/scop developers to get an idea if this service will be consistent and that the interface is relatively stable. Thanks, Dave

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Atom index
by Mike Liang 26 Jul '02

26 Jul '02

Hello! I found that if I open the same molecule twice (two models of same structure), the atom ordering in molecule.atoms are not the same between the two models. Is this correct? What is the best way to traverse the corresponding atoms in both molecules? I had expected the ordering of the .atoms to be the same ordering as in the PDB. Thanks, Mike

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osx
by Arthur.Glasfeld＠directory.reed.edu 23 Jul '02

23 Jul '02

Hi, This isn't a suggestion - just a question... Is there any likelihood of a chimera release for OSX on Macs? Thanks, Arthur Glasfeld

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Delphi
by Alexandra Schnoes 19 Jul '02

19 Jul '02

Hi, I've been trying to use the DelPhiController (on a linux machine) and discovered that /pub/share/delphi/exe/delphi has been hard-coded into the path. Since 'delphi' is what DelPhi calls the IRIX compiled code and 'delphiLinux' is what the linux compiled version is called, I am assuming that the DelPhiController can only be used on SGIs. Is this correct? If so may I heartily request the extension to linux. Many thanks! Alex -- Alexandra Schnoes Graduate Group in Biophysics University of California, San Francisco Tel: 415-502-5649 Fax: 415-476-6515 email: aschnoe(a)itsa.ucsf.edu

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Re: [chimera-dev] Accessing rotation matrix of molecule models
by Elaine Meng 19 Jul '02

19 Jul '02

Hello Mike, We haven't yet implemented the matrixget/matrixset commands that were in the predecessor program Midas. The write command just got implemented but is not in the released version (it will be in the next release). In the meanwhile, I can think of a few possibilities: (1) individual distances can be measured manually within Chimera ("distance" command or Controllers...Distances) (2) if you are on unix, the "pdbrun" command can be used to send out the coordinates of everything that is displayed. Note that the coordinates of both structures would be transformed, but you would be able to use these coordinate sets for the position of one relative to the other. The command would look something like pdbrun nouser cat > bothstructures.pdb You would have to make sure that all the atoms you want the coordinates of in the file bothstructures.pdb are displayed. All displayed models are in the output file, with END between them; you might need to make separate files out of this output file, depending on what you want to do next. (3) there is probably some not too complicated way to get and apply the transformation matrices out using the Python interface or a Python script, but I am not skilled in this area - other members of the development team could probably give you more details. I hope this helps. Anybody else with current solutions, please chime in... In the next version, I think the simplest way would be to use the "write" command to save the coordinates of one model relative to those of the other. Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, R.Ph., Ph.D. Babbitt Lab and Computer Graphics Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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Accessing rotation matrix of molecule models
by Mike Liang 18 Jul '02

18 Jul '02

Hello, Is there a way to access the rotation matrix of the molecular models? I'm interested in comparing/aligning two structures and I would like the user to rotate the models until they think it looks good. Then I want to compute the distance between the atoms, but I'd need to know what they're coordinates are in the same space. So is there a way to get the rotation matrix? Along with that, is there then a way to set the rotation matrix for a model? Thanks, Mike

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Minutes from Chimera meeting
by Conrad Huang 11 Jul '02

11 Jul '02

Notes from our Chimera meeting today are available via the web at https://www.cgl.ucsf.edu:8000/intranet/chimeradevelopment/2002-07-11.html If you want to add topics to the agenda for the next meeting, please e-mail them to me so I don't forget to add them in. Conrad

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Chimera-dev July 2002