[phenixbb] Simulated anneal

Qiang Chen chen at red.dfci.harvard.edu
Tue Nov 13 17:33:30 PST 2012

Hi all,

I have a 3.05Å structure. I refine it to Rwork=25.2 Rfree=28.81. I use
Molprobity to check the structure. The clash score is 100th and Molprobity
score is 99th.  I was suggested to run simulated anneal to help reduce
Rwork and Rfree. I tried Cartesian and Torsion and different seed. The
best result I got is: torsion anneal, start_temp=2500,final_temp=300,
random_seed=4250146. The Rwork:25.8, Rfree=31.2. I checked the new model
and found that some places in a domain were not correctly traced. The
density for that domain is not good and have several flexible loops.  My
question is: does simulated anneal always work and reduce Rwork/Rfree?  At
the final stage of refinement, does it necessary to use simulated anneal



The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

More information about the phenixbb mailing list