[phenixbb] phenix.cut_out_density problem

Anastasia A Aksyuk aaksyuk at bio.purdue.edu
Thu Aug 25 10:27:16 PDT 2011


Hi everyone,
I am trying the phenix.cut_out_density. It fails with the error message 
below. How can I specify "the bigger version"? or what else could I try?

Actually, I have a set of scripts using ccp4 programs (from 
http://www.phaser.cimr.cam.ac.uk/index.php/Using_Electron_Density_as_a_Model) 
which can do the same thing, but I thought it would be nice to use 
something simpler. Too bad it fails.

Thanks,
Anastasia


Reading model density histograms from 
/apps/phenix/phenix-1.7.1-743/solve_resolve/ext_ref_files/segments/rho.list
Read total of            6 sets of density functions
Sorry, need to increase n_asym_unit_max. Try a bigger version

***************************************************
Sorry, this version does not seem big enough...
  (Current value of isizeit is  48)
You might try increasing "isizeit" by using a bigger version (giant/huge)
You might try cutting back the resolution
You might try "unlimit" allow full use of memory
***************************************************

resolve exit_info:
   source_file: 
/net/longnose/scratch2/phenix/phenix-1.7.1-743/solve_resolve/resolve/need_coarse_grid.cpp
   source_line: 59
   status: 13
Trying size of ... 96 ...
Possibly cresolve size 96 was too big for this machine

Resolve failed

Error messages:




Could not run resolve with size 96


COMMANDS USED:
pdb_in_memory
no_build
mask_cycles 1
minor_cycles 0
no_build
  cutout
  fine_grid
  no_sort
resolution 1000 12.0
cell1 15.0 15.0 15.0 90 90 90
cutout_center 130.2186526 85.5323180106 9.50263752826
padding 5.0
cutout_mask 1
cutout_sphere 10.0
rad_mask 5.0



************************************************
Resolve error message:



Could not run resolve with size 96


************************************************



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