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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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RE: test version of chimera (fwd)
by Greg Couch 25 Jun '02

25 Jun '02

Comments from Jeff Blaney on the gcc 3.1 linux version. The msms problem is the same one that was fixed on the other platforms recently. Greg ---------- Forwarded message ---------- Date: Fri, 21 Jun 2002 23:53:42 -0700 From: Jeff Blaney <jeff_blaney(a)stromix.com> To: Greg Couch <gregc(a)cgl.ucsf.EDU> Subject: RE: test version of chimera Hi, Greg Finally had a chance to try it out. At a quick glance, seems ok, except that it complains it can't load MSMS when I try to generate a surface. I like the low resolution view in the side window; I suggest you make it the default. I noticed there is a now a report of the RMS fit from a match command, but you should round the value to only 2 significant figures. I also noticed that the model box no longer shows the directory name leading to the model; I'd prefer to see the paths relative the directory from which chimera was launched. Jeff

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two things
by Elaine Meng 24 Jun '02

24 Jun '02

Hello, (1) re Jeff's comments, I agree about there being too many digits shown for RMS values that show up in the status line. I don't know that there should only be two, but I think right now 5-6 digits after the decimal are shown, which is way too many. He did not say WHY he preferred the low resolution version of the Side View, but I am guessing it is a performance issue rather than esthetics. Regardless of which is the default, perhaps it could be in the Preferences so that one does not have to change it to the preferred setting every time Chimera is used. (2) I note that the background color of the HTML pages credits.html and embedded.html in the docs directory changed to white. I strongly urge that we change it back to "nothing" since all of the other pages linked to the documentation index, as well as the documentation index, are NOT white and now things are inconsistent. This includes the Programmer's Guide and User's Guide, so it would not make sense to make everything white. Thanks, Elaine

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Chimera
by Markus Winter 11 Jun '02

11 Jun '02

Hi, any chance of a MacOS X version? Best Regards Markus -- Dr. Markus Winter Tel: 0064 (0)9 373 7599 (wait for message then type extension) 3960

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gzipped PDB files
by Mike Liang 06 Jun '02

06 Jun '02

Hi! Can you guys allow opening of gzipped PDB files? Or alternatively open a 'string' that contains the contents from a PDB file. This way i'll just do something like data=gzip.open('filename').read() and feed data into the open command (kind of how you guys do 'VRML'). Thanks, Mike

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Chimera development discussion minutes
by Conrad Huang 08 May '02

08 May '02

I'm going to try to start writing down some of our discussions during our Thursday Chimera meetings. My first stab at the current issues may be found at https://www.cgl.ucsf.edu:8000/intranet/chimeradevelopment/2002-04-18.html There is also a link from the intranet page to the list of available pages (currently one :-). If I've left off an issue, please let me know and I will revise. Conrad

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Chimera Text Protocols
by Eric Pettersen 06 May '02

06 May '02

I've implemented the interface changes that standardize capitalization and so forth that we agreed on in one of our meetings a while back (http://www. cgl.ucsf.edu/home/meng/frameprotocol.html) The only substantive change was the reorganization of the Help menu. The remaining changes were principally case changes and adding/subtracting colons and whatnot. --Eric

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Chimera stuff
by Elaine Meng 02 May '02

02 May '02

Hi Ed, You're welcome! >* Why can you "surface ligand", but not "select ligand"? Most commands accept an atom specification, but ligand/main/etc. are surface categories, not atom specs. Of course, that is just a restatement of your observation that "ligand" does not work as an atom spec. The surface categories were developed since there needed to be reasonable groupings for surface calculation, a whole different issue than whose surface is actually displayed. For example, if you surface a molecule such as biotin that is considered "ligand," the surface actually encloses the biotin, but if you surface some random residue in the protein, Chimera "knows" it is part of "main" and only shows surface where the residue is at the surface of the main protein. Thus surface *creation* would use the categories, but then *display* of the surface could use either categories as a whole, or atom specs, which could be subparts of categories. When using all those commands that use atom specs, I agree it might be convenient to also allow ligand/main/etc. to be atom specifications. The programmers on the team would need to think about this a bit more, in case there are ramifications. For now, you could use the atom spec @/surfaceCategory=ligand >* Automatic chain break detection would be really helpful. Currently, >Chimera connects all the residues in a chain, even when it's clear from the >bond length that there must be a chain break. Check out the command "longbond" - it should do the trick. There should not be a lot of long bonds in PDB standard-compliant files. They will occur in segments of missing density, but their presence does inform you that there is no chain break in reality, just missing density. Also, it is pretty easy to just use longbond if you want them to go away. The command can take parameters, but in practice I have never needed to specify them; I just use "longbond" with no arguments. Hope this helps! 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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more good points from Ed Boas
by Elaine Meng 02 May '02

02 May '02

The email below makes some good points. I can answer that "ligand" etc. are surface categories and not atom specs, but it does beg the question of why we couldn't make them usable as atom specs. The possible answer to the second item is that so far, we have focused more on handling correct PDB files, not various pathological cases. However, I am not sure what is supposed to happen in a correct PDB file when part of a chain is lacking density (e.g. a chain with residues 1-20 lacking density for residues in the middle...is there supposed to be a TER card in that case?). Comments on these issues welcome. Thanks, Elaine -------------------------------------------------------------------- >From boas(a)stanford.edu Thu May 2 14:10:18 2002 Date: Thu, 02 May 2002 14:10:13 -0700 To: Elaine Meng <meng(a)cgl.ucsf.EDU> From: "F. Edward Boas" <boas(a)stanford.edu> Subject: Re: Chimera issues/questions Hi Elaine, I wasn't expecting such a quick reply ... thanks! I have a couple more suggestions: * Why can you "surface ligand", but not "select ligand"? * Automatic chain break detection would be really helpful. Currently, Chimera connects all the residues in a chain, even when it's clear from the bond length that there must be a chain break. Thank you! Cheers, Ed ________________________________________________________________________ F. Edward Boas Phone: 650-787-1688 P.O. Box 17890 Email: boas(a)post.harvard.edu Stanford, CA 94309 Web: http://www.stanford.edu/~boas

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chimera-dev mailing list under mailma
by Conrad Huang 01 May '02

01 May '02

I've changed chimera-dev from a plain mailing list to a "mailman" mailing list, just to see how well mailman works. You can visit http://www.cgl.ucsf.edu/mailman/listinfo to see a web interface. Let me know what you think. Conrad PS This is only the second list I've created, so some things may not be working properly.

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