Re: [phenixbb] Problem avoiding real space refinement

27 Oct 2011

      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 
Nwachukwumailto:[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