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Hi Tofayel,<br>
<br>
<blockquote
cite="mid:PS1PR01MB0764554513A5EC7FBF86DD41E38F0@PS1PR01MB0764.apcprd01.prod.exchangelabs.com"
type="cite">
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<div id="divtagdefaultwrapper"
style="font-size:12pt;color:#000000;font-family:Calibri,Arial,Helvetica,sans-serif;"
dir="ltr">My phenix.real_space_refine run crashes with the error
mentioned below when I have used following command to run it on
a�complete ribosome (containing coordinates for small subunit
and large subunit in a single pdb�file):
<p><span>phenix.real_space_refine model.pdb map.mrc
resolution=4.5 reference_coordinate_restraints.enabled=true
reference_coordinate_restraints.selection="chain A and
resseq 2:700" reference_coordinate_restraints.sigma=0.05
secondary_structure.enabled=True res.eff > out.out</span><br>
</p>
<p><span><br>
</span></p>
<p><span>From the out.out file I can see that, it ran for 5
macro_cycles�and started group b-factor refinement which
reads�(last few lines):</span></p>
<p><span><br>
</span></p>
<p><span></span></p>
<div>|-----------------------------------------------------------------------------|</div>
<div>|-group b-factor refinement (macro cycle = 0; iterations =
0)-----------------|</div>
<div>| r_work = 0.3809 r_free = 0.3809 target = 0.153923
restraints weight = None �|</div>
<div>|-----------------------------------------------------------------------------|</div>
<div>|-group b-factor refinement (macro cycle = 1; iterations =
32)----------------|</div>
<div>| r_work = 0.3687 r_free = 0.3687 target = 0.144348
restraints weight = 1067.479|</div>
<div>|-----------------------------------------------------------------------------|</div>
<div>|-group b-factor refinement (macro cycle = 2; iterations =
37)----------------|</div>
<div>| r_work = 0.3724 r_free = 0.3724 target = 0.147257
restraints weight = 482.176|</div>
<div>|-----------------------------------------------------------------------------|</div>
<div>|-group b-factor refinement (macro cycle = 3; iterations =
32)----------------|</div>
<div>| r_work = 0.3747 r_free = 0.3747 target = 0.149066
restraints weight = 262.900|</div>
<div>|-----------------------------------------------------------------------------|</div>
<br>
<p><span>The run crashes at this point....</span></p>
</div>
</blockquote>
<br>
It crashes trying to refine B-factors in reciprocal space (which is
not the best idea anyway, I mean using reciprocal space for this,
but that's at we have at present!).<br>
So, please disable B factor refinement by adding this to your
command line: "run=minimization_global" (by default it is
"run=minimization_global+adp").<br>
<br>
<blockquote
cite="mid:PS1PR01MB0764554513A5EC7FBF86DD41E38F0@PS1PR01MB0764.apcprd01.prod.exchangelabs.com"
type="cite">
<div id="divtagdefaultwrapper"
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dir="ltr">
<p><span></span>However, phenix.real_space_refine runs fine when
I am refining�a�protein chain or a complex�(for eg: just the
large or the�small subunit of a�ribosome). Does it have to do
with my pdb file being so big after merging of both subunits
where I have also crossed 99999 atoms and atom serial
numbers�start from A0000?</p>
</div>
</blockquote>
<br>
No, it has nothing to do with this.<br>
<br>
<blockquote
cite="mid:PS1PR01MB0764554513A5EC7FBF86DD41E38F0@PS1PR01MB0764.apcprd01.prod.exchangelabs.com"
type="cite">
<div id="divtagdefaultwrapper"
style="font-size:12pt;color:#000000;font-family:Calibri,Arial,Helvetica,sans-serif;"
dir="ltr">
<p> A related question: What is the�latest consensus of using
chain IDs and atom serial numbers to use
in�phenix.real_space_refine for handling large files like
ribosome pdbs�? I have found some information on:�<a
moz-do-not-send="true" href="http://cci.lbl.gov/hybrid_36/"
class="OWAAutoLink" id="LPlnk576142" previewremoved="true">http://cci.lbl.gov/hybrid_36/</a></p>
</div>
</blockquote>
<br>
Using hybrid36 and two-letter chain IDs allows to fit into PDB
virtually any size model. Such files work fine across Phenix and
some good graphics programs. But PDB would not like these files.
Since PDB files will go away anyway with mmCIF being replacement,
I'd say best is to use mmCIF that can fit any size models too and
are supported in/out across Phenix.<br>
<br>
Tools to convert PDB <> mmCIF:<br>
<br>
phenix.cif_as_pdb<br>
phenix.pdb_as_cif<br>
<br>
Please let us know should you have more questions or need any help!<br>
<br>
Pavel<br>
<br>
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