- Chimera-dev - RBVI Mailing Lists

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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