[phenixbb] Random seeds?

Thomas C. Terwilliger terwilliger at lanl.gov
Tue Aug 10 16:22:30 PDT 2010

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: noel at salk.edu
>> Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37
>> Web Site (HHMI): http://hhmi.org/research/investigators/noel.html
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