congratulations to the new beta release
Hello, I have been writing to you before and you may remember that we communicated a bit about chimera. Now I have found the improved version on your www pages and would like to congratulate you on that. I especially like the new columns in the "model panel" with those checkboxes. What I still find missing is the option to display atom numbers (as taken from the input file) as labels. This can often be handy, for example when defining rotatable bonds in small molecules for docking studies, or when editing pdb files by hand. Best regards, Chris Klein -- Dr. C. Klein; cklein(at)pharma.anbi.ethz.ch Dept. of Applied Biosciences, Pharmaceutical Chemistry Swiss Federal Institute of Technology / ETH Zuerich Winterthurerstr. 190 CH-8057 Zuerich Phone: +41 1 6356062 FAX : +41 1 6356884
On Sunday, August 11, 2002, at 05:25 AM, C. Klein wrote:
Hello,
I have been writing to you before and you may remember that we communicated a bit about chimera. Now I have found the improved version on your www pages and would like to congratulate you on that. I especially like the new columns in the "model panel" with those checkboxes.
Hi Chris, Naturally I remember since the checkboxes were your idea! I guess it slipped my mind to send you a note when the 1516 release was out that included them. Glad you like them.
What I still find missing is the option to display atom numbers (as taken from the input file) as labels. This can often be handy, for example when defining rotatable bonds in small molecules for docking studies, or when editing pdb files by hand.
We will probably do something to accommodate this. The Chimera programmers will likely have to get together and have a discussion since there are some issues: not all input sources have serial numbers (e.g. gaussian files); preservation of serial numbering on output (probably can't; if atoms get added to a structure there may be no way to preserve the numbering [serial numbers are by definition monotonically increasing]). Once we decide how we want to proceed, then implementation shouldn't be too hard. Feel free to let us know about any other things you might want/need. Probably nothing would have happened about serial numbers if you hadn't said something -- no one else had yet mentioned needing it. Good to hear from you again, btw. --Eric
I forgot to ask something: do you use the Midas emulator much? Would you need to be able to use Midas atom specifiers to refer to atoms by serial number? [if you don't know what atom specifiers are, then the answer is no :-) ] Would you need to label atoms with serial numbers via some command in the Midas emulator? Would being able to label by serial number just via the Actions menu be sufficient for your needs? --Eric On Sunday, August 11, 2002, at 05:25 AM, C. Klein wrote:
Hello,
I have been writing to you before and you may remember that we communicated a bit about chimera. Now I have found the improved version on your www pages and would like to congratulate you on that. I especially like the new columns in the "model panel" with those checkboxes. What I still find missing is the option to display atom numbers (as taken from the input file) as labels. This can often be handy, for example when defining rotatable bonds in small molecules for docking studies, or when editing pdb files by hand.
Best regards,
Chris Klein
-- Dr. C. Klein; cklein(at)pharma.anbi.ethz.ch Dept. of Applied Biosciences, Pharmaceutical Chemistry Swiss Federal Institute of Technology / ETH Zuerich Winterthurerstr. 190 CH-8057 Zuerich Phone: +41 1 6356062 FAX : +41 1 6356884 _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Hi Eric, hmm, Midas.... I have used this "command language" and also the "atom specifiers" once in a while, but not too often. In general, I find it useful to have such a thing (because it allows you to simplify/automatize certain tasks). The problem is, as always, that I am reluctant to learn yet another "language". Concerning the specific problem of numbers and atom specifiers: it would certainly be sufficient for my purposes to access this function via the menu. I think that most other modeling programs have this display option, thus I am probably not the only person that needs it. If you were to ask me about general future wishes, then a "build molecule" and "write file" functionality would be on top of the wishlist. I know that this would be a major project. You would first have to decide on the file format: pdb is probably the most generic one. The swisspdb-viewer team decided on an extension to the pdb format (SPDPV lines added to the bottom of a regular pdb file) which contains spdbv-specific information on display and selection status. That is a good idea, because it allows you to read that particular file with practically all other modeling programs. The mol2 format is probably much more difficult to implement, but would be the second most important on my list, because it has become sort of a "lingua franca" for small molecules, and because it contains so many useful possibilities to store information. It is also the preferred (or the only possible!) input for all the "independent" docking programs (dock, autodock, gold ....). I am just having a major problem to connect accelrys software and these docking programs because accelrys "ignores" the mol2 format, that is giving me a big headache.... Best wishes, Chris
Hi Chris, Just a couple of further thoughts. As Elaine pointed out, the next release of Chimera (late October) will have saving-to-PDB available via the midas "write" command. Depending on other priorities, I may have to time to implement it also as a button in the model panel in time for the release, otherwise that will be in the following release. Saving sessions is now available in the "File" menu, though structure modifications (e.g. bond rotations) aren't saved in sessions yet. Saving to mol2 will also get done in the not-too-distant future, but mostly likely not by the next release. Maybe 50/50 for the following release. We have no plans to implement real structure building. We do allow swapping of amino acid / nucleic acid side chains via the midas "swapaa/swapna" commands, which still need some improvement though. Good structure building is a lot of work and other packages (e.g. Spartan, ChemDraw) do it so well that we'd prefer to work on things other packages don't have rather than re-invent a very round wheel. I guess this is kind of similar to the Delphi thing where we felt that it was better to integrate to an excellent external implementation rather than expend the many man-months necessary to make an implementation of similar quality in Chimera. In this case we wouldn't integrate per se but instead just suggest getting some package that does structure building and read the structure into Chimera normally. Whenever any other suggestions occur to you, make sure to drop us a line! --Eric On Thursday, August 15, 2002, at 12:12 AM, C. Klein wrote:
Hi Eric,
hmm, Midas.... I have used this "command language" and also the "atom specifiers" once in a while, but not too often. In general, I find it useful to have such a thing (because it allows you to simplify/automatize certain tasks). The problem is, as always, that I am reluctant to learn yet another "language".
Concerning the specific problem of numbers and atom specifiers: it would certainly be sufficient for my purposes to access this function via the menu. I think that most other modeling programs have this display option, thus I am probably not the only person that needs it.
If you were to ask me about general future wishes, then a "build molecule" and "write file" functionality would be on top of the wishlist. I know that this would be a major project. You would first have to decide on the file format: pdb is probably the most generic one. The swisspdb-viewer team decided on an extension to the pdb format (SPDPV lines added to the bottom of a regular pdb file) which contains spdbv-specific information on display and selection status. That is a good idea, because it allows you to read that particular file with practically all other modeling programs.
The mol2 format is probably much more difficult to implement, but would be the second most important on my list, because it has become sort of a "lingua franca" for small molecules, and because it contains so many useful possibilities to store information. It is also the preferred (or the only possible!) input for all the "independent" docking programs (dock, autodock, gold ....). I am just having a major problem to connect accelrys software and these docking programs because accelrys "ignores" the mol2 format, that is giving me a big headache....
Best wishes,
Chris _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
participants (2)
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C. Klein -
Eric Pettersen