Hi All, Okay, a fairly mundane question concerning random seeds in Phenix. Obviously they are random but any restrictions on how many digits phenix will accept? Any other restrictions? Are they (it) only used for coordinate refinement or do the random seeds get used for other things as well? I know about hydrogen building but wandering about other refinement protocols and the use of "new" random seeds. I realize some use different random seeds to create slightly different models after refinement. Is it useful to change the number from time to time when going through iterative rounds of re-building and coordinate refinement? What about ADP refinement? Sorry for the mundane questions! Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: [email protected] Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________
Okay, a fairly mundane question concerning random seeds in Phenix. Obviously they are random but any restrictions on how many digits phenix will accept?
It is determined by the random number generators we're using. Up to 9 digits should be fine. I'm not quite sure what the exact limit is.
Any other restrictions?
Don't think so. Any integer up to a certain limit should work.
Are they (it) only used for coordinate refinement
Any time the weight calculation is involved random numbers enter through the assignment of random velocities for a short Cartesian dynamics calculation. This is used to "shake" the model before computing x-ray/neutron gradients and restraint gradients. The weight is determined as the ratio of the norms of these gradients (after outlier removal).
or do the random seeds get used for other things as well?
The weight calculation and Cartesian or torsion-angle simulated annealing are the main uses. Beyond that it takes a closer look to know if random numbers enter into a particular procedure. Ralf
Hi Joe, In addition to what Ralf mentioned, if you are using phenix.autobuild the random seed is used there as well. However as you are starting from a different model each time, I would expect that you would not gain by changing the random seed (but the results would be different with a different random seed). All the best, Tom T
Hi All,
Okay, a fairly mundane question concerning random seeds in Phenix. Obviously they are random but any restrictions on how many digits phenix will accept? Any other restrictions? Are they (it) only used for coordinate refinement or do the random seeds get used for other things as well? I know about hydrogen building but wandering about other refinement protocols and the use of "new" random seeds. I realize some use different random seeds to create slightly different models after refinement. Is it useful to change the number from time to time when going through iterative rounds of re-building and coordinate refinement? What about ADP refinement?
Sorry for the mundane questions!
Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA
Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: [email protected]
Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Joseph Noel
-
Ralf W. Grosse-Kunstleve
-
Thomas C. Terwilliger