following this discussion, I was wondering how much sense it makes to use
TLS domains and experimental phases at the same time.
My take on it is that if you have low resolution data, then it makes a
good deal of sense to use both experimental phases and TLS groups. But
this assumes that the TLS groups are being used in place of per-residue
or per-atom B-factors, not in addition to them.
But my normal way of thinking about this is in terms of observations to
parameters at low resolution (not model completeness), so your mileage
may vary.
Pete
I would have thought that TLS domains are better to be used when the model is
fairly complete at which state the quality of the experimental phases are
probably outrun by those of the model unless the experimental phases are
_really_ good.
What is people's opinion about this?
Cheers, Tim
On Mon, Oct 11, 2010 at 11:48:15AM -0700, Ethan Merritt wrote:
On Monday, October 11, 2010 01:04:49 pm Christian Roth wrote:
Dear Ethan,
thanks for your fast answer. The pdb file does the trick. I also did not click
the reset B-factor box, which I thought is equivalent to the TLS+Biso pdb. Is
that wrong?
For what you are doing, it is correct to not click the box.
I just wanted to confirm what were the steps leading to the observed failure.
Every program has his special requirements and I mixed it up with a refinement
done some weeks before in phenix.
So far as I know, there is still no provision in phenix for reading in
existing TLS parameters. It always wants to regenerate them for itself.
This make it very hard, if not impossible, to compare refinement protocols
or validate previous refinements.
Ethan
I'm sorry about that and thanks again for your help
Christian
Am Montag 11 Oktober 2010 19:50:10 schrieb Ethan Merritt:
On Monday, October 11, 2010 11:01:10 am Christian Roth wrote:
Dear all,
I want refine my model using TLS plus phase information from experimental
phases.
I used the TLSMD server to generate the initial tls parameters and
started Refmac
I don't know exactly what has gone wrong.
Let's collect some more information.
- When you took the intial TLS parameters from TLSMD server, did you also
take the corresponding modified PDB file?
If not, that could well be the problem.
- It looks from the output that you did not tick the "reset B factors to
20" box in ccp4i. Can you confirm that?
Ethan
After an initial round of TLS refinement Refmac stops and and claims a
problem but nevertheless writes at the end "Task completed successfully"
and does not write any file despite it claims to have it done. I copied a
part of the log file at the end of the mail
Could anyone point me to the mistake i made probably?
Thanks in advance
Christian
#CCP4I VERSION CCP4Interface 2.0.6
#CCP4I SCRIPT LOG refmac5
#CCP4I DATE 11 Oct 2010 17:37:30
#CCP4I USER roth
#CCP4I PROJECT sharpoutputrefinement
#CCP4I JOB_ID 19
#CCP4I SCRATCH /tmp
#CCP4I HOSTNAME bbzws339.bbz.uni-leipzig.de
#CCP4I PID 13018
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
###############################################################
###############################################################
###############################################################
### CCP4 6.1: Refmac_5.5.0109 version 5.5.0109 : 13/10/09##
###############################################################
User: unknown Run date: 11/10/2010 Run time: 17:37:30
Please reference: Collaborative Computational Project, Number 4. 1994.
"The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50,
760-763.
as well as any specific reference in the program write-up.
<!--SUMMARY_END--></FONT></B>
$TEXT:Reference1: $$ comment $$
"Refinement of Macromolecular Structures by the Maximum-Likelihood
Method:" G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
Acta Crystallogr. D53, 240-255
EU Validation contract: BIO2CT-92-0524
$$
$SUMMARY :Reference1: $$ Refmac: $$
:TEXT:Reference1: $$
Data line--- make check NONE
Data line--- make hydrogen ALL hout NO peptide NO
cispeptide NO ssbridge YES symmetry YES sugar YES
connectivity NO link NO
Data line--- refi type REST PHASE SCBL BBLU resi MLKF
meth CGMAT bref ISOT
Data line--- refi tlsc 10
Data line--- ncyc 25
Data line--- scal type SIMP LSSC ANISO EXPE
Data line--- solvent YES
Data line--- weight MATRIX 0.1
Data line--- monitor MEDIUM torsion 10.0 distance 10.0
angle 10.0 plane 10.0 chiral 10.0 bfactor 10.0 bsphere
10.0 rbond 10.0 ncsr 10.0
Data line--- labin FP=FP SIGFP=SIGFP HLA=HLA HLB=HLB HLC=HLC HLD=HLD
FREE=FreeR_flag
Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT
PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB
Data line--- PNAME sharpoutputrefinement
Data line--- DNAME hrsync
Data line--- RSIZE 80
Data line--- END
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename:
/homes/roth/dlhdata/sharp/eden_unique.mtz
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename:
/software/linuxsoft/ccp4/ccp4-6.1.3/lib/data/syminfo.lib
**** Input and Default parameters# ****
Input coordinate file. Logical name - XYZIN actual file name -
/homes/roth/dlhdata/sharp/shrefmac9.pdb
Output coordinate file. Logical name - XYZOUT actual file name -
/homes/roth/dlhdata/sharp/shrefmac10.pdb
Input reflection file. Logical name - HKLIN actual file name -
/homes/roth/dlhdata/sharp/eden_unique.mtz
Output reflection file. Logical name - HKLOUT actual file name -
/homes/roth/dlhdata/sharp/eden_refmac3.mtz
Cell from mtz : 61.560 69.500 133.350 90.000 90.000
90.000 Space group from mtz: number - 19; name - P 21 21 21
Refinement type : Restrained
***TLS refinement cycle*** 2
1
0.1153065 0.1254572 0.1168760 1.2506233E-02
2.1331017E-03 1.5424690E-04
-1.4598943E-02 -3.3578421E-03 -1.7373050E-02 -3.3114674E-03
-1.3628958E-02 -2.4346421E-03
-8.4016532E-02 4.1347187E-02 -0.1191208 -0.1013065 -0.1222848
0.1371335 -0.2420141 5.1373582E-02
-0.3787168
Problem
xyz 1107 48.64835 38.25826 83.76399 -34.85817
8.685342 -6.930134 -12.26284 -18.79212 3.157892
19.69073 -34.85817 0.6871372 23.66340 -0.3420097
-0.5949482 0.7273692
*************************************************************************
** * Information from CCP4Interface script
*************************************************************************
** Writing final coordinates (XYZOUT) to
/homes/roth/dlhdata/sharp/shrefmac10.pdb
*************************************************************************
**
*************************************************************************
** * Information from CCP4Interface script
*************************************************************************
** Writing final phases (HKLOUT) to
/homes/roth/dlhdata/sharp/eden_refmac3.mtz
*************************************************************************
**
*************************************************************************
** * Information from CCP4Interface script
*************************************************************************
** Writing final TLS (TLSOUT) to
/homes/roth/dlhdata/sharp/dlhtls_refmac1.tls
*************************************************************************
**
#CCP4I TERMINATION STATUS 1
#CCP4I TERMINATION TIME 11 Oct 2010 17:42:38
#CCP4I TERMINATION OUTPUT_FILES
/homes/roth/dlhdata/sharp/sharpoutputrefinement_19_hrsync.refmac.cif
sharpoutputrefinement
#CCP4I MESSAGE Task completed successfully
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
