August 2002 - Chimera-dev - RBVI Mailing Lists

ryle
by Greg Couch 28 Aug '02

28 Aug '02

It appears that someone reinstalled chimera on ryle and that blew away all of the development only stuff in the Chimera installation tree. Please don't ever do that again. Thanks, Greg

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a reminder about arnauld
by Greg Couch 23 Aug '02

23 Aug '02

Please keep the arnauld console logged in as administrator so bilbo, the linux development host, can continue to run. If for some reason you do log out as administrator, you need to first go to the vmware bilbo window and shutdown bilbo by logging into bilbo as root and running shutdown. The problem when someone logs out the administrator is that there is a chance that bilbo's disks will get trashed unless it is brought down cleanly first. (FYI, the fsck was successful, and I don't need to know who logged out without bringing bilbo down first.) This problem is getting worse where someone wants to use arnauld to demo/debug and someone needs arnauld/bilbo to build the Linux distribution, so I'd like to get bilbo moved to another computer, preferably a linux server in the machine room running linux natively (ASAP). Greg

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congratulations to the new beta release
by C. Klein 22 Aug '02

22 Aug '02

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

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Re: [chimera-dev] congratulations to the new beta release
by Elaine Meng 15 Aug '02

15 Aug '02

Hi Chris, The "write file" capability is actually already implemented in our working version and will be available in the next release (likely in the neighborhood of Oct/Nov). The man page for that command is http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html Basically, you will be able to write a PDB file of a model in transformed or untransformed coordinates. 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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hydrogen optimization
by Terry Downing 14 Aug '02

14 Aug '02

Hi, I am attempting to add hydrogens to proteins with ligands bound...I am using the AddH extension, which appears to add hydrogens with reasonable bond lengths and bond angles...However, I notice that because default torsion angles are being used, there are situations in which the cartesian coordinates of the hydrogens are not optimized and result in clashes...This is particularly a problem with hydrogens that are attached to heavy atoms that are free to rotate (ie methyl and amide groups)...Are there any torsion minimization protocols available where I can optimize the torsional angle of just the newly added hydrogens without changing the cartesian coordinates of the heavy atoms (allow them to rotate to optimize the hydrogen placement but not move away from the experimental coordinates)?...I just spoke with Tom Ferrin and he said that Eric was the person most experienced with the AddH extension, and he recommended that I look at the documentation from both him and Elaine...Anything you can recommend on this would be greatly appreciated... Sincerely, P. Therese Downing Kuntz Lab

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Re: [chimera-dev] hydrogen optimization
by Elaine Meng 14 Aug '02

14 Aug '02

Hello, Currently there is no "force field" functionality within Chimera, and thus no minimization/dynamics. At this point you would need to use AMBER or SYBYL to perform those types of calculations. We plan to have such capability in the future, but it is a nontrivial operation. 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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meeting reminder
by Conrad Huang 08 Aug '02

08 Aug '02

There will be a Chimera meeting at 1:30 in S922 today. The agenda is at https://wwwtest.cgl.ucsf.edu/intranet/chimeradevelopment/agenda.html Conrad

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Re: [chimera-dev] writing pdb files
by Elaine Meng 02 Aug '02

02 Aug '02

Dear Jim, If you have a UNIX system, the "pdbrun" command may be able to do what you want. Only the transformed coordinates are written out. I recommend the "nouser" keyword to avoid getting a lot of extra information in USER records. If there are multiple models, they all get sent to one file with END records in between (some postprocessing may be required). example usage: pdbrun all nouser cat >file.pdb See http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pdbrun.html The "write" command is much better for this purpose (and works for all of the platforms) but is not in the current release. It has been implemented in our working version and will be available in the next release. See http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html I am not sure when the next release will come out, however. Finally, I believe there is a way to get the transformation matrices but I must defer to the programmers on the team to address this point. I 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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writing pdb files
by J. H. Prestegard 02 Aug '02

02 Aug '02

I hope commands to write out pdb files for trandformed molecules (or the transformation matrices) will be implemented soon. Since we do additional calculations on files transformed by commands such as match, these are very important tools for us. Jim Prestegard

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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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Chimera-dev August 2002