Problem avoiding real space refinement
Hi: We noticed that in some of our refinements, real space refinement was performed even though we chose not to do this. I tried to opt out of real space refinement as follows: " refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp *tls *occupancies group_anomalous ..." however, the R-free is identical whether we select real space refinement or not, and the logfile shows " Validate: |--------START--------| |--------FINAL--------| residue map_cc 2mFo-DFc mFo-DFc map_cc 2mFo-DFc mFo-DFc "LYS A 18 " 0.9359 16.78 0.00 0.9107 17.60 0.00 "ARG A 19 " 0.9513 21.82 0.00 0.9470 20.97 -6.52 <<< "ARG A 26 " 0.9440 26.72 0.00 0.9474 27.33 -2.43 "ARG A 69 " 0.9685 31.36 0.00 0.9659 32.58 0.00 "GLN A 86 " 0.9681 23.57 -5.81 0.8850 19.29 -18.27 <<< "GLU A 89 " 0.9689 26.30 -4.43 0.8977 23.67 -11.59 <<< "LYS A 93 " 0.9746 25.19 0.00 0.9682 26.47 2.90 ... " and suggesting that real space refinement was performed. Is there a way to correct this, or to ensure that real space refinement is not performed during refinement? Thank you, -Jerome Jerome C. Nwachukwu, PhD Dept. of Cancer Biology The Scripps Research Institute-Florida
On Thu, Oct 27, 2011 at 8:31 AM, Jerome Nwachukwu
We noticed that in some of our refinements, real space refinement was performed even though we chose not to do this. I tried to opt out of real space refinement as follows: " refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp *tls *occupancies group_anomalous ..." however, the R-free is identical whether we select real space refinement or not, and the logfile shows " Validate: |--------START--------| |--------FINAL--------| residue map_cc 2mFo-DFc mFo-DFc map_cc 2mFo-DFc mFo-DFc "LYS A 18 " 0.9359 16.78 0.00 0.9107 17.60 0.00 "ARG A 19 " 0.9513 21.82 0.00 0.9470 20.97 -6.52 <<< "ARG A 26 " 0.9440 26.72 0.00 0.9474 27.33 -2.43 "ARG A 69 " 0.9685 31.36 0.00 0.9659 32.58 0.00 "GLN A 86 " 0.9681 23.57 -5.81 0.8850 19.29 -18.27 <<< "GLU A 89 " 0.9689 26.30 -4.43 0.8977 23.67 -11.59 <<< "LYS A 93 " 0.9746 25.19 0.00 0.9682 26.47 2.90 ... " and suggesting that real space refinement was performed.
That's the rotamer fitting - technically, it's an independent step (fix_rotamers=True) The individual_sites_real_space strategy only performs global real-space refinement. -Nat
Hi, yes, this is exactly it. Sorry, I keep promising to clean this naming/conception mess one day. Hopefully (thanks Herb), this day is approaching fast! Pavel On 10/27/11 8:51 AM, Nathaniel Echols wrote:
We noticed that in some of our refinements, real space refinement was performed even though we chose not to do this. I tried to opt out of real space refinement as follows: " refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp *tls *occupancies group_anomalous ..." however, the R-free is identical whether we select real space refinement or not, and the logfile shows " Validate: |--------START--------| |--------FINAL--------| residue map_cc 2mFo-DFc mFo-DFc map_cc 2mFo-DFc mFo-DFc "LYS A 18 " 0.9359 16.78 0.00 0.9107 17.60 0.00 "ARG A 19 " 0.9513 21.82 0.00 0.9470 20.97 -6.52<<< "ARG A 26 " 0.9440 26.72 0.00 0.9474 27.33 -2.43 "ARG A 69 " 0.9685 31.36 0.00 0.9659 32.58 0.00 "GLN A 86 " 0.9681 23.57 -5.81 0.8850 19.29 -18.27<<< "GLU A 89 " 0.9689 26.30 -4.43 0.8977 23.67 -11.59<<< "LYS A 93 " 0.9746 25.19 0.00 0.9682 26.47 2.90 ... " and suggesting that real space refinement was performed. That's the rotamer fitting - technically, it's an independent step (fix_rotamers=True) The individual_sites_real_space strategy only
On Thu, Oct 27, 2011 at 8:31 AM, Jerome Nwachukwu
wrote: performs global real-space refinement. -Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Interesting. I've also noticed that lines (such as those shown below) are missing from the logfiles whether I select *individual_sites_real_space or not.
|-LOCKIT real space refinement (target=simple): start-------------------------|
| r_work=0.2098 r_free=0.2283 rmsd bonds=0.004 angles= 1.03 |
|-----------------------------------------------------------------------------|
|-LOCKIT real space refinement (target=simple): end---------------------------|
| r_work=0.2203 r_free=0.2521 rmsd bonds=0.004 angles= 0.74 |
|-----------------------------------------------------------------------------|
Could it be that the global *individual_sites_real_space strategy was actually not performed in either case? I would be glad to send you the logfiles off list, if that would be more helpful.
Thank you,
-Jerome
Jerome C. Nwachukwu, PhD
Nettles' Lab
Dept. of Cancer Biology
Scripps-FL
x3297
On Oct 27, 2011, at 1:12 PM, Pavel Afonine wrote:
Hi,
yes, this is exactly it. Sorry, I keep promising to clean this
naming/conception mess one day. Hopefully (thanks Herb), this day is
approaching fast!
Pavel
On 10/27/11 8:51 AM, Nathaniel Echols wrote:
On Thu, Oct 27, 2011 at 8:31 AM, Jerome Nwachukwu
Hi Jerome, I can't reproduce this myself. I just run it and I can see the output like you quote below in both - the log file and terminal screen. Can you possibly send me the complete reproducer (all inputs and commands necessary to reproduce the problem, and explain in details what you did to obtain this problem)? Pavel On 10/27/11 10:42 AM, Jerome Nwachukwu wrote:
Interesting. I've also noticed that lines (such as those shown below) are missing from the logfiles whether I select *individual_sites_real_space or not.
|-LOCKIT real space refinement (target=simple): start-------------------------| | r_work=0.2098 r_free=0.2283 rmsd bonds=0.004 angles= 1.03 | |-----------------------------------------------------------------------------|
|-LOCKIT real space refinement (target=simple): end---------------------------| | r_work=0.2203 r_free=0.2521 rmsd bonds=0.004 angles= 0.74 | |-----------------------------------------------------------------------------|
Could it be that the global *individual_sites_real_space strategy was actually not performed in either case? I would be glad to send you the logfiles off list, if that would be more helpful. Thank you,
-Jerome Jerome C. Nwachukwu, PhD Nettles' Lab Dept. of Cancer Biology Scripps-FL x3297
On Oct 27, 2011, at 1:12 PM, Pavel Afonine wrote:
Hi,
yes, this is exactly it. Sorry, I keep promising to clean this naming/conception mess one day. Hopefully (thanks Herb), this day is approaching fast!
Pavel
On 10/27/11 8:51 AM, Nathaniel Echols wrote:
We noticed that in some of our refinements, real space refinement was performed even though we chose not to do this. I tried to opt out of real space refinement as follows: " refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp *tls *occupancies group_anomalous ..." however, the R-free is identical whether we select real space refinement or not, and the logfile shows " Validate: |--------START--------| |--------FINAL--------| residue map_cc 2mFo-DFc mFo-DFc map_cc 2mFo-DFc mFo-DFc "LYS A 18 " 0.9359 16.78 0.00 0.9107 17.60 0.00 "ARG A 19 " 0.9513 21.82 0.00 0.9470 20.97 -6.52<<< "ARG A 26 " 0.9440 26.72 0.00 0.9474 27.33 -2.43 "ARG A 69 " 0.9685 31.36 0.00 0.9659 32.58 0.00 "GLN A 86 " 0.9681 23.57 -5.81 0.8850 19.29 -18.27<<< "GLU A 89 " 0.9689 26.30 -4.43 0.8977 23.67 -11.59<<< "LYS A 93 " 0.9746 25.19 0.00 0.9682 26.47 2.90 ... " and suggesting that real space refinement was performed. That's the rotamer fitting - technically, it's an independent step (fix_rotamers=True) The individual_sites_real_space strategy only
On Thu, Oct 27, 2011 at 8:31 AM, Jerome Nwachukwu
mailto:[email protected]> wrote: performs global real-space refinement. -Nat _______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
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Jerome Nwachukwu
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Nathaniel Echols
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Pavel Afonine