[modeller_usage] problems modeling a multimer

[Douglas Kojetin <>]

Hi All,

I would like create a hexameric model using a target sequence and a  
hexameric PDB template.  I am trying to create an alignment using  
input files that have the \ character to separate the chains.  Example:

>P1;target
sequence:target:::::::0.00: 0.00
AAAAA\
BBBBB\
CCCCC\
DDDDD\
EEEEE\
FFFFF*

I'm using the align2d.py example, as detailed in tutorial 2.  My  
input PDB file has six chains (A-F).  My align2d.py file is as follows:

""" align2d.py START
from modeller import *
log.verbose()
env = environ()
aln = alignment(env)
mdl = model(env, file='PDBfile_hexamer', model_segment= 
('FIRST:A','LAST:F'))
aln.append_model(mdl, align_codes='PDBfile_hexamer',  
atom_files='PDBfile_hexamer.pdb')
aln.append(file='target_hexamer.ali', align_codes='target')
aln.align2d()
aln.write(file='target_hexamer-PDBfile_hexamer.ali',  
alignment_format='PIR')
aln.write(file='target_hexamer-PDBfile_hexamer.pap',  
alignment_format='PAP')
"""align2d.py END

Using modeller9v1 (linux RPM), I started the above calculation  
(python align2d.py), but it has not finished after 20 hours (and is  
still going; 100% CPU and 22.6% memory usage out of 3 GB total,  
according to 'top').  Although I used log.verbose(), there is very  
little output in the associated log (see below).

Any ideas?

Thanks,
Doug



""" LOG START

                         MODELLER 9v1, 2007/01/19, r4822

     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS


                     Copyright(c) 1989-2007 Andrej Sali
                            All Rights Reserved

                             Written by A. Sali
                               with help from
           B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,
                N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser,
                    R. Sanchez, B. Yerkovich, A. Badretdinov,
                      F. Melo, J.P. Overington, E. Feyfant
                 University of California, San Francisco, USA
                    Rockefeller University, New York, USA
                      Harvard University, Cambridge, USA
                   Imperial Cancer Research Fund, London, UK
              Birkbeck College, University of London, London, UK


Kind, OS, HostName, Kernel, Processor: 4, Linux carbo.msbb.uc.edu  
2.6.18-1.2869.fc6 i686
Date and time of compilation         : 2007/01/19 13:47:34
MODELLER executable type             : i386-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2007/05/11 11:26:27

openf___224_> Open           $(LIB)/restyp.lib
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL9v1}/modlib/ 
resgrp.lib
rdresgr_266_> Number of residue groups:        2
openf___224_> Open           ${MODINSTALL9v1}/modlib/sstruc.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:       
3216122    3140.744     3.067

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:       
3216650    3141.260     3.068
openf___224_> Open           ${MODINSTALL9v1}/modlib/resdih.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:       
3265250    3188.721     3.114
rdrdih__263_> Number of dihedral angle types         :        9
              Maximal number of dihedral angle optima:        3
              Dihedral angle names                   :  Alph Phi Psi  
Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open           ${MODINSTALL9v1}/modlib/radii.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:       
3280562    3203.674     3.129
openf___224_> Open           ${MODINSTALL9v1}/modlib/radii14.lib
openf___224_> Open           ${MODINSTALL9v1}/modlib/solv.lib
openf5__224_> Open       11  OLD  SEQUENTIAL  ${MODINSTALL9v1}/modlib/ 
af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes:  APBLE
openf___224_> Open           ${MODINSTALL9v1}/modlib/mnch.lib
rdclass_257_> Number of classes:        5
openf___224_> Open           ${MODINSTALL9v1}/modlib/mnch1.lib
openf___224_> Open           ${MODINSTALL9v1}/modlib/mnch2.lib
openf___224_> Open           ${MODINSTALL9v1}/modlib/mnch3.lib
openf___224_> Open           ${MODINSTALL9v1}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types:       21
runcmd______> model.read(file='PDBfile_hexamer', (def) 
model_format='PDB', model_segment=('FIRST:A', 'LAST:F'))
openf___224_> Open           PDBfile_hexamer.pdb

Dynamically allocated memory at       amaxmodel [B,KiB,MiB]:       
7756771    7574.972     7.397
openf___224_> Open           PDBfile_hexamer.pdb
read_mo_297_> Segments, residues, atoms:       24     4818    38574
read_mo_298_> Segment:        1     4 A   234 A     1790
read_mo_298_> Segment:        2   246 A   271 A      214
read_mo_298_> Segment:        3   291 A   636 A     2799
read_mo_298_> Segment:        4   651 A   850 A     1626
read_mo_298_> Segment:        5     4 B   234 B     1790
read_mo_298_> Segment:        6   246 B   271 B      214
read_mo_298_> Segment:        7   291 B   636 B     2799
read_mo_298_> Segment:        8   651 B   850 B     1626
read_mo_298_> Segment:        9     4 C   234 C     1790
read_mo_298_> Segment:       10   246 C   271 C      214
read_mo_298_> Segment:       11   291 C   636 C     2799
read_mo_298_> Segment:       12   651 C   850 C     1626
read_mo_298_> Segment:       13     4 D   234 D     1790
read_mo_298_> Segment:       14   246 D   271 D      214
read_mo_298_> Segment:       15   291 D   636 D     2799
read_mo_298_> Segment:       16   651 D   850 D     1626
read_mo_298_> Segment:       17     4 E   234 E     1790
read_mo_298_> Segment:       18   246 E   271 E      214
read_mo_298_> Segment:       19   291 E   636 E     2799
read_mo_298_> Segment:       20   651 E   850 E     1626
read_mo_298_> Segment:       21     4 F   234 F     1790
read_mo_298_> Segment:       22   246 F   271 F      214
read_mo_298_> Segment:       23   291 F   636 F     2799
read_mo_298_> Segment:       24   651 F   850 F     1626
relabel_387W> Model has multiple chains, and they do not all have a  
unique
              chain ID. Suggest you relabel them as A, B, C, etc.
runcmd______> alignment.append_model 
(atom_files='PDBfile_hexamer.pdb', align_codes='PDBfile_hexamer')

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       
7896464    7711.391     7.531

Dynamically allocated memory at   amaxstructure [B,KiB,MiB]:      
10639518   10390.154    10.147
runcmd______> alignment.append(align_codes=['PDBfile_hexamer',  
'target'], atom_files=['PDBfile_hexamer.pdb'],  
file='target_hexamer.ali', (def)remove_gaps=True, (def) 
alignment_format='PIR', (def)rewind_file=False, (def)close_file=True)
openf___224_> Open           target_hexamer.ali

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      
12123550   11839.404    11.562

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      
13607494   13288.568    12.977

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:      
13607522   13288.596    12.977

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:      
13607550   13288.623    12.977

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:      
13607578   13288.650    12.977

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:      
13607606   13288.678    12.977

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:      
13607634   13288.705    12.977

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:      
13627070   13307.686    12.996

Read the alignment from file       : target_hexamer.ali
Total number of alignment positions:  4865

  #  Code        #_Res #_Segm PDB_code    Name
------------------------------------------------------------------------ 
-------
  1  PDBfile_hexa    4818     24 PDBfile_hexame undefined
  2       target    4860      6        target
runcmd______> alignment.align2d((def)overhang=0, (def)align_block=0,  
(def)rr_file='$(LIB)/as1.sim.mat', (def)align_what='BLOCK', (def) 
off_diagonal=100, (def)max_gap_length=999999, (def) 
local_alignment=False, (def)matrix_offset=0.0, (def)gap_penalties_1d= 
(-900.0, -50.0), (def)gap_penalties_2d=(3.5, 3.5, 3.5,  
0.20000000000000001, 4.0, 6.5, 2.0, 0.0, 0.0), (def)surftyp=1, (def) 
fit=True, (def)fix_offsets=(0.0, -1.0, -2.0, -3.0, -4.0), (def) 
read_weights=False, (def)write_weights=False, (def) 
input_weights_file='', (def)output_weights_file='', (def)n_subopt=1,  
(def)subopt_offset=0.0, (def)read_profile=False, (def) 
input_profile_file='', (def)write_profile=False, (def) 
output_profile_file='', (def)weigh_sequences=False, (def) 
smooth_prof_weight=10, (def)weights_type='SIMILAR')
align2d_276_> 'align_block' changed to 1.
openf___224_> Open           PDBfile_hexamer.pdb

Dynamically allocated memory at   amaxstructure [B,KiB,MiB]:      
13627550   13308.154    12.996
openf___224_> Open           PDBfile_hexamer.pdb
mkapsa__637W> No residue topology library is in memory.
              Better radii would be used if topology.read() is  
called first.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
              Default CHARMM atom type assigned:  N -->  N
              This message is written only for the first such atom.
openf___224_> Open           $(LIB)/as1.sim.mat
rdrrwgh_268_> Number of residue types:       20
""" LOG END