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ccp4 / dimple

:large_blue_diamond: MX pipeline. Refinement and ligand screening.
http://ccp4.github.io/dimple/
Apache License 2.0
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Warning: passing input to render failed. #8

Closed Anthchirp closed 5 years ago

Anthchirp commented 5 years ago

dimple output:

(...)
 10 find-blobs       0.4s  Blob scores: 67 53
Rendering 2 largest blobs: at (-17.8, -10.7, -8.2) and at (-18.4, -10.3, 0.1)
 11 coot            12.8s  stdout: 4372 lines                                
 12 render           2.2s   blob1v1.png / 13 blob1v2.png / 14 blob1v3.png
 15 render           4.3s   blob2v1.png / 16
Warning: passing input to render failed.

 blob2v2.png
Error: render failed (exit status 255).
/dls_sw/apps/ccp4/7.0.065/ccp4-7.0/bin/render -png blob2v2.png < blob2v2.r3d

stderr:
-> 16-render.log

16-render.log says:

title="coot 0.8.9.1: Raster3D output"
Rendered raster size =    900 x    900
  Output raster size =    600 x    600

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %                      Raster3D    V3.0.3                      %
 %            --------------------------------------            %
 % If you publish figures generated by this program please cite %
 %   Merritt & Bacon (1997)  Meth. Enzymol. 277, 505-524.       %
 %            --------------------------------------            %
 %                  Raster3D distribution site                  %
 %          http://www.bmsc.washington.edu/raster3d/            %
 % comments & suggestions to:          merritt@u.washington.edu %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

 Expand DETAIL to      4000000
 ERROR >>>>>> too many object details - increase MAXDET and recompile

Dimple exits with a non-zero exit code which means we will treat the overall processing as failed.

final.mtz.gz dimple.log fast_dp.mtz.gz

wojdyr commented 5 years ago

Is it reproducible if you run it again? I have the same version of CCP4 but I didn't get this error:

     ### Dimple v2.5.9. Problems and suggestions: ccp4.github.io/dimple ###
MTZ (1.6A)            I 2 3        (77.95, 77.95, 77.95,  90, 90, 90)
3I40.pdb              I 21 3       (77.22, 77.22, 77.22,  90, 90, 90)
  1 rwcontents       0.0s  24 x 6kDa (+ 1kDa het) in 460nm3, 63% solvent
  2 pointless        1.4s  resol. 1.61 A   #refl: 10275
    [-k,h,l]   CC: 0.638    cell diff: 0.7A
    [h,k,l]    CC: 0.064    cell diff: 0.7A
reindexed MTZ         I 21 3       (77.95, 77.95, 77.95,  90, 90, 90)
  3 truncate         0.3s  B=27.1
Rigid-body refinement with resolution 3.5 A, 10 cycles. 0.7 waters/aa.
  4 refmac5 rigid    3.8s  10/10   R  0.2357  ->  0.2231
No MR for R < 0.4.
Generate free-R flags (repeatably)
  5 unique           0.2s  
  6 freerflag        0.5s  
  7 cad              0.3s  #refl  10275 -> 10302
Restrained refinement, 4+8 cycles.
  8 refmac5 jelly   14.9s   4/4   R/Rfree  0.3008/0.2873  ->  0.2221/0.2030
    RMS:   bond 0.016 -> 0.014   angle 1.35 -> 1.67   chiral 0.10 -> 0.11
  9 refmac5 restr   29.4s   8/8   R/Rfree  0.2173/0.1980  ->  0.1934/0.1902
    RMS:   bond 0.016 -> 0.013   angle 1.96 -> 1.77   chiral 0.13 -> 0.11
 10 find-blobs       0.3s  Blob scores: 67 53
Rendering 2 largest blobs: at (-17.8, -10.7, -8.2) and at (-18.4, -10.3, 0.1)
 11 coot             5.7s  stdout: 4380 lines                                 
 12 render           1.3s   blob1v1.png / 13 blob1v2.png / 14 blob1v3.png
 15 render           2.6s   blob2v1.png / 16 blob2v2.png / 17 blob2v3.png

and 16-render.log:

title="coot 0.8.9.1: Raster3D output"
Rendered raster size =    900 x    900
  Output raster size =    600 x    600

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %                      Raster3D    V3.0.3                      %
 %            --------------------------------------            %
 % If you publish figures generated by this program please cite %
 %   Merritt & Bacon (1997)  Meth. Enzymol. 277, 505-524.       %
 %            --------------------------------------            %
 %                  Raster3D distribution site                  %
 %          http://www.bmsc.washington.edu/raster3d/            %
 % comments & suggestions to:          merritt@u.washington.edu %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

 To center objects in rendered scene, change translation to:
   -0.1109    7.8232   18.3017
 Z limits (unscaled) before clipping:    -14.69     15.61
 Z-clipping limits:                       -9.00      3.00
 Fog (linear) limits, density:            -9.00      3.00      1.00
 -------------------------------
  spheres           =     992
  cylinders         =  163142
  Z-clipped objects =   92159
  total objects     =  164134
 -------------------------------
rendering time -     2 sec
wojdyr commented 5 years ago

I reproduced it on a different example and added a workaround. This error is a strange thing. It never happened when I tested Dimple a few years ago and Raster3D hasn't changed since then. Perhaps something changed in coot.