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Hi Pavel,<br>
<br>
Yes, I am specifiying .def files in the commands. The commands used are:<br>
1) phenix.refine input.mtz input.pdb strategy=rigid_body<br>
2) phenix.refine input_refine_002.def simulated_annealing=true<br>
3) phenix.refine input_refine_003.def ordered_solvent=true<br>
<br>
I send you the .def and .log files in a separate email.<br>
<br>
Thanks, Oliv<br>
<br>
<br>
Pavel Afonine wrote:
<blockquote cite="mid:49839947.5050705@lbl.gov" type="cite">
<pre wrap="">Hi Oliv,
I have a guess about what is wrong, but before I say it, could you
please send us the exact command you are using. IF you are specifying a
.def or .eff file in the command line, could you please send this .eff
or .def files as well.
Pavel.
On 1/30/2009 4:02 PM, Oliv Eidam wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
I am currently refining a good 1.6 Angstroem data set using Phenix.
Thereby I noticed a significant difference of R-free (>3%) depending on
whether I used phenix version 1.3-rc6 (installed on my Mac laptop) or
phenix version 1.4-3 (installed on my linux work station). Rfree differs
by more than 3% (!) although I am using the same starting model, the
same reflection file and the same refinement protocol (shown at the end
of this email with detailed R and R-free factors for the 3 steps).
In my opinion, my phenix 1.4-3 installation has a problem in the "bulk
solvent modeling and scaling" steps. Indeed, I find in the log file that
the "overall anisotropic scale matrix" shows all values set to zero.
Analogous the "maximum likelihood estimate for coordinate error". This
is true in all steps where an "overall anisotropic scale matrix" is
calculated.
Here is one example during 1.4-3 refinement:
====================== bulk solvent modeling and scaling
======================
|--(resolution: 1.61 - 29.59 A; n_refl. =
99535)------------------------------|
|
|
| r_work= 0.3419 r_free= 0.3358 ksol= 0.39 Bsol= 19.12 scale=
1.247 |
|
|
| overall anisotropic scale matrix (Cartesian basis;
B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3=
0.00 |
|
|
| maximum likelihood estimate for coordinate error: -0.00
A |
| x-ray target function (ml) for work reflections:
5.981207 |
|-----------------------------------------------------------------------------|
The same example during 1.3-rc6 refinement:
===================== bulk solvent correction and scaling
=====================
|-macro cycle = 1-(resolution: 1.61 - 29.59 A; n_refl. =
99537)---------------|
|
|
| r_work= 0.3153 r_free= 0.3064 ksol= 0.40 Bsol= 43.79 scale=
1.087 |
|
|
| overall anisotropic scale matrix (Cartesian basis;
B11,B22,B33,B12,B13,B23):|
| (-4.01,-5.36,-8.20,-0.00,2.74,0.00); trace/3=
-5.86 |
|
|
| maximum likelihood estimate for coordinate error: 0.33
A |
| x-ray target function (ml) for work reflections:
5.946583 |
|-----------------------------------------------------------------------------|
I am asking now: Did something go wrong during my Phenix installation? I
already re-installed Phenix (no errors): same result. Do I have to
change something in my input files? I should probably mention that
"bulk_solvent_and_scale = True" in my input .def files.
Any help appreciated. Many thanks,
Oliv
--------------------------------------------------------------------------------
Refinement protocol and development of R and Rfree during each
refinement round:
--------------------------------------------------------------------------------
1)Rigid body refinement
2) Simulated annealing (5000K)
3) Ordered solvent (plus annealing @ 2000K)
phenix version 1.3-rc6:
1) R=31.5, Rf=30.6
2) R=23.9, Rf=25.8
3) R=19.8, Rf=22.0
phenix version 1.4-3:
1) R=31.6, Rf=30.6
2) R=27.8, Rf=29.8
3) R=23.7, Rf=25.2
</pre>
</blockquote>
<pre wrap=""><!---->_______________________________________________
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Oliv Eidam, Ph.D.
Postdoctoral fellow
University of California, San Francisco
Dept. of Pharmaceutical Chemistry
1700 4th Street, Byers Hall North, Room 501
San Francisco, CA 94158 - Box 2550
Phone: 415-514-4253
Fax : 415-514-4260
Email: <a class="moz-txt-link-abbreviated" href="mailto:eidamo@blur.compbio.ucsf.edu">eidamo@blur.compbio.ucsf.edu</a>
</pre>
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