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 again? Thanks! yamei 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.
On Tue, Nov 13, 2012 at 5:33 PM, Qiang Chen
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?
No, especially when the structure is nearly finished.
At the final stage of refinement, does it necessary to use simulated anneal again?
Definitely not necessary. Simulated annealing is a good way to improve a model that fits the data poorly, or to remove model bias, but at the end of refinement you should be much more conservative. There are several other potential ways to reduce the R-free - such as using TLS, or optimizing the weights. But you already have excellent geometry and your R-free and R-free/R-work gap are both reasonable for that resolution, so it's possible that further refinement won't help. -Nat
Your R-values are already good enough (but make sure the density is traced correctly) No, simulated annealing does not always reduce Rfree. You just demonstrated that it does not. And no, not only it is not necessary to use simulated annealing in the final stages, it is completely counterproductive. You are supposedly already near the global minimum. On 11/13/2012 08:33 PM, Qiang Chen wrote:
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 again?
Thanks!
yamei
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.
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participants (3)
-
Ed Pozharski -
Nathaniel Echols -
Qiang Chen