No subject


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....


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? A related question: What is the latest consensus of using chai=
n IDs and atom serial numbers to use in phenix.real_space_refine for handli=
ng large files like ribosome pdbs ? I have found some information on: http:=
//cci.lbl.gov/hybrid_36/



The error in terminal reads:


Traceback (most recent call last):
  File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/comman=
d_line/real_space_refine.py", line 782, in <module>
    o =3D run(sys.argv[1:])
  File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/comman=
d_line/real_space_refine.py", line 518, in __init__
    self.caller(func =3D self.run_macro_cycles, prefix=3D"Macro-cycles")
  File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/comman=
d_line/real_space_refine.py", line 547, in caller
    status =3D func(prefix=3Dprefix, **kwargs)
  File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/comman=
d_line/real_space_refine.py", line 540, in run_macro_cycles
    log                         =3D self.log)
  File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/refinement/macr=
o_cycle_real_space.py", line 66, in __init__
    self.caller(self.refine_adp,                "ADP refinement")
  File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/refinement/macr=
o_cycle_real_space.py", line 71, in caller
    status =3D func(prefix=3Dprefix)
  File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/refinement/macr=
o_cycle_real_space.py", line 317, in refine_adp
    adp_refinery.refine()
  File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/refinemen=
t/real_space/adp.py", line 78, in refine
    b_isos_refined =3D self.refine_box_with_selected(selection=3Dsel)
  File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/refinemen=
t/real_space/adp.py", line 56, in refine_box_with_selected
    fmodel.update_all_scales(update_f_part1=3DFalse, apply_back_trace=3DTru=
e)
  File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f=
_model.py", line 1452, in update_all_scales
    self.apply_scale_k1_to_f_obs()
  File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f=
_model.py", line 1500, in apply_scale_k1_to_f_obs
    r_start =3D self.r_work()
  File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f=
_model.py", line 2004, in r_work
    selection  =3D selection)
  File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f=
_model.py", line 1972, in _r_factor
    f_model =3D self.f_model_scaled_with_k1_w().data()
  File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f=
_model.py", line 1730, in f_model_scaled_with_k1_w
    data       =3D self.scale_k1_w()*self.f_model_work().data())
  File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f=
_model.py", line 2048, in scale_k1_w
    selection=3Dselection)
  File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f=
_model.py", line 182, in _scale_helper
    raise RuntimeError("Zero denominator in scale calculation.")
RuntimeError: Zero denominator in scale calculation.



Best regards,

Tofayel

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<div id=3D"divtagdefaultwrapper" style=3D"font-size:12pt;color:#000000;font=
-family:Calibri,Arial,Helvetica,sans-serif;" dir=3D"ltr">
<p>Dear developers and users,</p>
<p><br>
</p>
<p>My phenix.real_space_refine run crashes with the error mentioned below w=
hen I have used following command to run it on a&nbsp;complete ribosome (co=
ntaining coordinates for small subunit and large subunit in a single pdb&nb=
sp;file):</p>
<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></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>
</span>
<p></p>
<p><span>The run crashes at this point....</span></p>
<p><span><br>
</span></p>
<p>However, phenix.real_space_refine runs fine when I am refining&nbsp;a&nb=
sp;protein chain or a complex&nbsp;(for eg: just the large or the&nbsp;smal=
l 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 A0000? A related quest=
ion: What is the&nbsp;latest consensus of using chain IDs and atom serial n=
umbers to use in&nbsp;phenix.real_space_refine for handling large files lik=
e ribosome pdbs&nbsp;? I have found some information
 on:&nbsp;<a href=3D"http://cci.lbl.gov/hybrid_36/" class=3D"OWAAutoLink" i=
d=3D"LPlnk576142" previewremoved=3D"true">http://cci.lbl.gov/hybrid_36/</a>=
</p>
<br>
<p><br>
</p>
<p>The error in terminal reads:</p>
<p><br>
</p>
<p></p>
<div>Traceback (most recent call last):</div>
<div>&nbsp; File &quot;/usr/local/phenix-1.11.1-2575/build/../modules/pheni=
x/phenix/command_line/real_space_refine.py&quot;, line 782, in &lt;module&g=
t;</div>
<div>&nbsp; &nbsp; o =3D run(sys.argv[1:])</div>
<div>&nbsp; File &quot;/usr/local/phenix-1.11.1-2575/build/../modules/pheni=
x/phenix/command_line/real_space_refine.py&quot;, line 518, in __init__</di=
v>
<div>&nbsp; &nbsp; self.caller(func =3D self.run_macro_cycles, prefix=3D&qu=
ot;Macro-cycles&quot;)</div>
<div>&nbsp; File &quot;/usr/local/phenix-1.11.1-2575/build/../modules/pheni=
x/phenix/command_line/real_space_refine.py&quot;, line 547, in caller</div>
<div>&nbsp; &nbsp; status =3D func(prefix=3Dprefix, **kwargs)</div>
<div>&nbsp; File &quot;/usr/local/phenix-1.11.1-2575/build/../modules/pheni=
x/phenix/command_line/real_space_refine.py&quot;, line 540, in run_macro_cy=
cles</div>
<div>&nbsp; &nbsp; log &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nb=
sp; &nbsp; &nbsp; &nbsp; &nbsp; =3D self.log)</div>
<div>&nbsp; File &quot;/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/=
refinement/macro_cycle_real_space.py&quot;, line 66, in __init__</div>
<div>&nbsp; &nbsp; self.caller(self.refine_adp, &nbsp; &nbsp; &nbsp; &nbsp;=
 &nbsp; &nbsp; &nbsp; &nbsp;&quot;ADP refinement&quot;)</div>
<div>&nbsp; File &quot;/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/=
refinement/macro_cycle_real_space.py&quot;, line 71, in caller</div>
<div>&nbsp; &nbsp; status =3D func(prefix=3Dprefix)</div>
<div>&nbsp; File &quot;/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/=
refinement/macro_cycle_real_space.py&quot;, line 317, in refine_adp</div>
<div>&nbsp; &nbsp; adp_refinery.refine()</div>
<div>&nbsp; File &quot;/usr/local/phenix-1.11.1-2575/modules/cctbx_project/=
mmtbx/refinement/real_space/adp.py&quot;, line 78, in refine</div>
<div>&nbsp; &nbsp; b_isos_refined =3D self.refine_box_with_selected(selecti=
on=3Dsel)</div>
<div>&nbsp; File &quot;/usr/local/phenix-1.11.1-2575/modules/cctbx_project/=
mmtbx/refinement/real_space/adp.py&quot;, line 56, in refine_box_with_selec=
ted</div>
<div>&nbsp; &nbsp; fmodel.update_all_scales(update_f_part1=3DFalse, apply_b=
ack_trace=3DTrue)</div>
<div>&nbsp; File &quot;/usr/local/phenix-1.11.1-2575/modules/cctbx_project/=
mmtbx/f_model/f_model.py&quot;, line 1452, in update_all_scales</div>
<div>&nbsp; &nbsp; self.apply_scale_k1_to_f_obs()</div>
<div>&nbsp; File &quot;/usr/local/phenix-1.11.1-2575/modules/cctbx_project/=
mmtbx/f_model/f_model.py&quot;, line 1500, in apply_scale_k1_to_f_obs</div>
<div>&nbsp; &nbsp; r_start =3D self.r_work()</div>
<div>&nbsp; File &quot;/usr/local/phenix-1.11.1-2575/modules/cctbx_project/=
mmtbx/f_model/f_model.py&quot;, line 2004, in r_work</div>
<div>&nbsp; &nbsp; selection &nbsp;=3D selection)</div>
<div>&nbsp; File &quot;/usr/local/phenix-1.11.1-2575/modules/cctbx_project/=
mmtbx/f_model/f_model.py&quot;, line 1972, in _r_factor</div>
<div>&nbsp; &nbsp; f_model =3D self.f_model_scaled_with_k1_w().data()</div>
<div>&nbsp; File &quot;/usr/local/phenix-1.11.1-2575/modules/cctbx_project/=
mmtbx/f_model/f_model.py&quot;, line 1730, in f_model_scaled_with_k1_w</div=
>
<div>&nbsp; &nbsp; data &nbsp; &nbsp; &nbsp; =3D self.scale_k1_w()*self.f_m=
odel_work().data())</div>
<div>&nbsp; File &quot;/usr/local/phenix-1.11.1-2575/modules/cctbx_project/=
mmtbx/f_model/f_model.py&quot;, line 2048, in scale_k1_w</div>
<div>&nbsp; &nbsp; selection=3Dselection)</div>
<div>&nbsp; File &quot;/usr/local/phenix-1.11.1-2575/modules/cctbx_project/=
mmtbx/f_model/f_model.py&quot;, line 182, in _scale_helper</div>
<div>&nbsp; &nbsp; raise RuntimeError(&quot;Zero denominator in scale calcu=
lation.&quot;)</div>
<div>RuntimeError: Zero denominator in scale calculation.</div>
<div><br>
</div>
<br>
<p></p>
<p>Best regards,</p>
<p>Tofayel</p>
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