I'm trying to do a loop refinement calculation with the dopehr_loopmodel class, modeller 9v4. Here's the python script I'm using: from modeller import * from modeller.automodel import * log.verbose() # request verbose output env = environ() # directories for input atom files env.io.atom_files_directory = ['./', 'PDB/'] a = dopehr_loopmodel(env, alnfile='TTN.ali', knowns='2g8gOligo', sequence='1s58', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 1 a.md_level = None # No refinement of model a.loop.starting_model = 1 a.loop.ending_model = 1 a.loop.md_level = refine.fast a.make()
After a few hours of running, it stop. Here's the last part of the log: ... randomi_498_> Atoms,selected atoms,random_seed,amplitude: 36972 36056 1 5.0000 randomi_496_> Amplitude is > 0; randomization is done. preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 327553569 319876.531 312.379
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 554709537 541708.562 529.012 preppdf_458W> Both Lennard-Jones and statistical potential terms selected. check_inf__E> Atom 31754 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated.
>> Summary of successfully produced models: Filename molpdf DOPE score GA341 score ---------------------------------------------------------------------- 1s58.B99990001.pdb 75059.09375 -361379.46875 0.78559
>> Summary of failed loop models: 1s58.BL00010001.pdb check_inf__E> Atom 31754 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated.
Dynamically allocated memory at finish [B,KiB,MiB]: 549216697 536344.438 523.774 Starting time : 2008/10/24 10:37:24 Closing time : 2008/10/24 12:51:48 Total CPU time [seconds] : 8018.72
The model part went OK, but when it tried to do the loop refinement it went crazy (the coordinates in1s58.BL00010001.pdb are all messed up).
I'm also testing the other two classes (loopmodel and dope_loopmodel) and they've been running for a long while now, so I don't know if they'll work or not. I'd just like to know if I'm doing something wrong or I just ran into some kind of glitch or bug in the dopehr algorithm.
Thanks!
-- 0 | Mauricio Carrillo Tripp, PhD / | Department of Molecular Biology, TPC6 0 | The Scripps Research Institute \ | 10550 North Torrey Pines Road
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