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Re: [modeller_usage] loops iterations and various DOPE scores

Here are the last lines of a typical log file. This run stopped after reading 236 files out of 1000 loop files. I have finished all of what I wanted to do by reading the files in smaller batches. In all cases the log files record a similar memory problem 


openf5__224_> Open       11  OLD  SEQUENTIAL  ABC31_HUMAN.BL02370001.pdb
Dynamically allocated memory at amaxstructure [B,kB,MB]: -669621493 -653927.250 -638.601 
openf5__224_> Open       11  OLD  SEQUENTIAL  ABC31_HUMAN.BL02370001.pdb

transfe_506_> MODEL is an average of all templates.
transfe_511_> Number of templates for coordinate transfer:        1
After transfering coordinates of the equivalent template atoms, 
             there are defined, undefined atoms in MODEL:     4312        0

Model assessment by DOPE potential

iatmcls_286W> MODEL atom not classified:  SER:OXT  SER
runcmd______> model.energy((def)deviation=0.0, (def)asgl_output=False, normalize_profile=True, residue_span_range=(1, 999 ), output='ENERGY_PROFILE NO_REPORT', file='RPE65_HUMAN.BL02370001.pdb\n.profile', (def)output_directory='', smoothing_wi dow=15, (def)viol_report_cut=(4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 4.5, 999, 999, 999, 999, 4.5, 4 5, 4.5, 4.5, 4.5, 4.5, 999, 6.5, 4.5, 4.5, 4.5, 4.5, 4.5, 999, 999, 999, 4.5, 4.5), (def)viol_report_cut2=(2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2 0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0), schedule_scale=[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0 0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0]) 

preppdf_453W> No fixed restraints selected; there may be some dynamic ones.
preppdf_454W> Restraints file was probably not read; use restraints.append().
Dynamically allocated memory at amaxhash_contac [B,kB,MB]: -668379505 -652714.375 -637.416
Dynamically allocated memory at amaxrestraints [B,kB,MB]: -668276025 -652613.312 -637.318
Dynamically allocated memory at amaxrestraints [B,kB,MB]: -668172537 -652512.250 -637.219
Dynamically allocated memory at amaxrestraints [B,kB,MB]: -667965561 -652310.125 -637.022
Dynamically allocated memory at amaxrestraints [B,kB,MB]: -667551609 -651905.875 -636.627
Dynamically allocated memory at amaxrestraints [B,kB,MB]: -666723705 -651097.375 -635.837
Dynamically allocated memory at amaxrestraints [B,kB,MB]: -665067897 -649480.375 -634.258 
alloc_r_215E> Dynamic memory allocation failed.
             Routine, variable, status:  iapairs         2



On screen the following is echoed:


*** malloc: vm_allocate(size=6623232) failed (error code=3)
*** malloc[601]: error: Can't allocate region

Modeller 8v1 is running on a MAC G5 running OSX version 10.3.


Thanks,

Starr
--On Tuesday, December 06, 2005 07:56:24 PM -0800 Modeller Caretaker <> wrote: 


Starr Hazard wrote:

I am having several difficulties with analysis of my loops.

I built a model and selected a region to refine as a loop.

I have successfully created 1000 loop files.

Based on the model_energies.py file from the examples, I am attempting
to scan the 1000 loop model files.


Sounds OK so far.


def dope_profile(mdl, file):
   # DOPE energy parameters
   edat = energy_data(contact_shell=15.0, dynamic_modeller=True,
                      dynamic_lennard=False, dynamic_sphere=False,
                      excl_local=(False, False, False, False))
   # DOPE group restraints
   oldgprsr = mdl.group_restraints
   if not model.dope_restraints:
       model.dope_restraints = \
           group_restraints(classes='${LIB}/atmcls-mf.lib',
                            parameters='${LIB}/dist-mf.lib')
   mdl.group_restraints = model.dope_restraints
   molpdf = mdl.energy(output='SHORT', file=file,
                       edat=edat, residue_span_range=(1, 9999),
                       normalize_profile=True, smoothing_window=10)
   mdl.group_restraints = oldgprsr
   return molpdf


You actually only need this routine if you're using Modeller 8v0. 8v1 can
produce a profile from the 'assess_dope' routine (see below). Makes the
script a bit more readable. ;)


filename = 'loop.list'
in_file = open(filename,"r")
while 1:
   # read model file
   code = in_file.readline()
   mdl = model(env)
   mdl.read(file=code)
   aln = alignment(env)
   # generate topology
   aln.append_model(mdl, atom_files=code, align_codes=code)
   aln.append_model(mdl, atom_files=code, align_codes=code+'-ini')
   mdl.generate_topology(aln, sequence=code+'-ini')
   mdl.transfer_xyz(aln)


Presumably all of your loop models were built with the same Modeller
inputs, so the sequence of every model should be the same. In this case,
you can take all of this code outside of the loop, and just put the
mdl.read call within it. That should give you the same results in less
time.


1a) So, Is there a limit to ability of Modeller or python to handle long
file name strings?


Python has no limit. Modeller (due to Fortran limitations) is in some
cases limited to 600 characters, and will truncate file names if they're
longer than this.


1b) Why am I not able to digest all 1000 loop models?


What's the error you get?


2) In the log file that's produced I see a line like this for the first
loop model:

DOPE  score      :-51270.746094

What is the relationship between the summed per residue values from the
profile output (ie -15.0456) and this DOPE score from the log file?


There is no direct relationship, as the per-residue values are divided by
the number of restraints acting on each residue.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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