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Mon Jul 25 12:19:07 PDT 2016


|--------------------------------------------------------------------------=
---|
|-group b-factor refinement (macro cycle =3D 0; iterations =3D 0)----------=
-------|
| r_work =3D 0.3809 r_free =3D 0.3809 target =3D 0.153923 restraints weight=
 =3D None  |
|--------------------------------------------------------------------------=
---|
|-group b-factor refinement (macro cycle =3D 1; iterations =3D 32)---------=
-------|
| r_work =3D 0.3687 r_free =3D 0.3687 target =3D 0.144348 restraints weight=
 =3D 1067.479|
|--------------------------------------------------------------------------=
---|
|-group b-factor refinement (macro cycle =3D 2; iterations =3D 37)---------=
-------|
| r_work =3D 0.3724 r_free =3D 0.3724 target =3D 0.147257 restraints weight=
 =3D 482.176|
|--------------------------------------------------------------------------=
---|
|-group b-factor refinement (macro cycle =3D 3; iterations =3D 32)---------=
-------|
| r_work =3D 0.3747 r_free =3D 0.3747 target =3D 0.149066 restraints weight=
 =3D 262.900|
|--------------------------------------------------------------------------=
---|


The run crashes at this point....

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!).
So, please disable B factor refinement by adding this to your command line:=
 "run=3Dminimization_global" (by default it is "run=3Dminimization_global+a=
dp").


However, phenix.real_space_refine runs fine when I am refining a protein ch=
ain 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 s=
ubunits where I have also crossed 99999 atoms and atom serial numbers start=
 from A0000?

No, it has nothing to do with this.


A related question: What is the latest consensus of using chain IDs and ato=
m serial numbers to use in phenix.real_space_refine for handling large file=
s like ribosome pdbs ? I have found some information on: http://cci.lbl.gov=
/hybrid_36/

Using hybrid36 and two-letter chain IDs allows to fit into PDB virtually an=
y size model. Such files work fine across Phenix and some good graphics pro=
grams. But PDB would not like these files. Since PDB files will go away any=
way 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.

Tools to convert PDB <> mmCIF:

phenix.cif_as_pdb
phenix.pdb_as_cif

Please let us know should you have more questions or need any help!

Pavel


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1">
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<body dir=3D"ltr">
<div id=3D"divtagdefaultwrapper" style=3D"font-size:12pt;color:#000000;font=
-family:Calibri,Arial,Helvetica,sans-serif;" dir=3D"ltr">
<p><span style=3D"color: rgb(0, 111, 201);">Hi Pavel,</span></p>
<p><br>
</p>
<p><span style=3D"color: rgb(0, 111, 201);">Thanks so much for your reply !=
 Disabling the&nbsp;b-factor refinement solved my problem.&nbsp;</span></p>
<div></div>
<p></p>
<p><br>
</p>
<div id=3D"Signature"><span style=3D"color: rgb(0, 111, 201);"></span>
<div id=3D"divtagdefaultwrapper" style=3D"font-size:12pt; font-family:Calib=
ri,Arial,Helvetica,sans-serif; background-color:rgb(255,255,255)">
<span style=3D"color: rgb(0, 111, 201);"></span>
<p style=3D"color:rgb(0,0,0)"><span style=3D"color: rgb(0, 111, 201);">Best=
 regards,</span></p>
<span style=3D"color: rgb(0, 111, 201);"></span>
<p style=3D"color:rgb(0,0,0)"><span style=3D"color: rgb(0, 111, 201);">Tofa=
yel</span></p>
<p style=3D"color:rgb(0,0,0)"><span style=3D"font-size: 12pt;">&nbsp;&nbsp;=
</span><br>
</p>
<p style=3D"color:rgb(0,0,0)"></p>
<p style=3D"color:rgb(0,0,0)"></p>
<p style=3D"color:rgb(0,0,0)"><span style=3D"font-size:12pt"></span></p>
</div>
</div>
<br>
<br>
<div style=3D"color: rgb(0, 0, 0);">
<hr tabindex=3D"-1" style=3D"display:inline-block; width:98%">
<div id=3D"divRplyFwdMsg" dir=3D"ltr"><font face=3D"Calibri, sans-serif" co=
lor=3D"#000000" style=3D"font-size:11pt"><b>From:</b> Pavel Afonine &lt;paf=
onine at lbl.gov&gt;<br>
<b>Sent:</b> Thursday, December 1, 2016 11:22 PM<br>
<b>To:</b> #AHMED TOFAYEL#; PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] phenix.real_space_refine crashes for very la=
rge pdb files</font>
<div>&nbsp;</div>
</div>
<div>Hi Tofayel,<br>
<br>
<blockquote type=3D"cite">
<div id=3D"divtagdefaultwrapper" dir=3D"ltr" style=3D"font-size:12pt; color=
:#000000; font-family:Calibri,Arial,Helvetica,sans-serif">
My phenix.real_space_refine run crashes with the error mentioned below when=
 I have used following command to run it on a&nbsp;complete ribosome (conta=
ining coordinates for small subunit and large subunit in a single pdb&nbsp;=
file):
<p><span>phenix.real_space_refine model.pdb map.mrc resolution=3D4.5 refere=
nce_coordinate_restraints.enabled=3Dtrue reference_coordinate_restraints.se=
lection=3D&quot;chain A and resseq 2:700&quot; reference_coordinate_restrai=
nts.sigma=3D0.05 secondary_structure.enabled=3DTrue
 res.eff &gt; 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&nb=
sp;and started group b-factor refinement which reads&nbsp;(last few lines):=
</span></p>
<p><span><br>
</span></p>
<p><span></span></p>
<div>|---------------------------------------------------------------------=
--------|</div>
<div>|-group b-factor refinement (macro cycle =3D 0; iterations =3D 0)-----=
------------|</div>
<div>| r_work =3D 0.3809 r_free =3D 0.3809 target =3D 0.153923 restraints w=
eight =3D None &nbsp;|</div>
<div>|---------------------------------------------------------------------=
--------|</div>
<div>|-group b-factor refinement (macro cycle =3D 1; iterations =3D 32)----=
------------|</div>
<div>| r_work =3D 0.3687 r_free =3D 0.3687 target =3D 0.144348 restraints w=
eight =3D 1067.479|</div>
<div>|---------------------------------------------------------------------=
--------|</div>
<div>|-group b-factor refinement (macro cycle =3D 2; iterations =3D 37)----=
------------|</div>
<div>| r_work =3D 0.3724 r_free =3D 0.3724 target =3D 0.147257 restraints w=
eight =3D 482.176|</div>
<div>|---------------------------------------------------------------------=
--------|</div>
<div>|-group b-factor refinement (macro cycle =3D 3; iterations =3D 32)----=
------------|</div>
<div>| r_work =3D 0.3747 r_free =3D 0.3747 target =3D 0.149066 restraints w=
eight =3D 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:=
 &quot;run=3Dminimization_global&quot; (by default it is &quot;run=3Dminimi=
zation_global&#43;adp&quot;).<br>
<br>
<blockquote type=3D"cite">
<div id=3D"divtagdefaultwrapper" dir=3D"ltr" style=3D"font-size:12pt; color=
:#000000; font-family:Calibri,Arial,Helvetica,sans-serif">
<p><span></span>However, phenix.real_space_refine runs fine when I am refin=
ing&nbsp;a&nbsp;protein chain or a complex&nbsp;(for eg: just the large or =
the&nbsp;small subunit of a&nbsp;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&nbsp;start from A000=
0?</p>
</div>
</blockquote>
<br>
No, it has nothing to do with this.<br>
<br>
<blockquote type=3D"cite">
<div id=3D"divtagdefaultwrapper" dir=3D"ltr" style=3D"font-size:12pt; color=
:#000000; font-family:Calibri,Arial,Helvetica,sans-serif">
<p>A related question: What is the&nbsp;latest consensus of using chain IDs=
 and atom serial numbers to use in&nbsp;phenix.real_space_refine for handli=
ng large files like ribosome pdbs&nbsp;? I have found some information on:&=
nbsp;<a href=3D"http://cci.lbl.gov/hybrid_36/" class=3D"OWAAutoLink" id=3D"=
LPlnk576142" previewremoved=3D"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 an=
y size model. Such files work fine across Phenix and some good graphics pro=
grams. But PDB would not like these files. Since PDB files will go away any=
way with mmCIF being replacement,
 I'd say best is to use mmCIF that can fit any size models too and are supp=
orted in/out across Phenix.<br>
<br>
Tools to convert PDB &lt;&gt; 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>
</div>
</div>
</div>
</body>
</html>

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