Hi Anastasia,

Hmmm...I'm sorry for the trouble!  It looks to me as though something failed and that the error message about memory is not the actual problem, as your cell is not big and your resolution is very low.

Could you possibly send me ([email protected], not the list) the exact input files and the cut_out_density.eff  parameters file that was generated by this run (or your input script file if you used a script)?  I will be happy to figure out what happened if you can do that.

All the best,
Tom T
 


On Aug 25, 2011, at 11:27 AM, Anastasia A Aksyuk wrote:

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


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

_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb


Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: [email protected]
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss