Hi,
i generated a model using the model_single.py example. So this is without loop modeling. Now I would like to model loops only, using the example from the manual:
from modeller import * from modeller.automodel import *
class my_lm(dope_loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): return selection(self.residue_range('535', '562'))
env = environ() a = my_lm(env, alnfile='HsMhc1_best_no_loops_motor.ali', knowns='1DFK_motor', sequence='HsMhc1')
a.starting_model = 1 a.ending_model = 1 a.md_level = None # No refinement of model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 5 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level
a.make()
Please note that I used the dope_loopmodel class instead of loopmodel as indicated in the manual. When I run the script, it exits with the following message:
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 1 68 111 445 496 671 602 791 874 924 1041
<< end of ENERGY. iatmcls_286W> MODEL atom not classified: GLU:OXT GLU preppdf_458W> Both Lennard-Jones and statistical potential terms selected. preppdf_458W> Both Lennard-Jones and statistical potential terms selected. preppdf_458W> Both Lennard-Jones and statistical potential terms selected. check_inf__E> Atom 4293 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated.
Using dopehr_loopmodel gives the same error whereas the "old" loopmodel works. Here is the Atom record from the PDB file:
ATOM 4293 N LEU 535 10.568 18.659 81.951 1.00103.06 1SG4294
The coordinates do not seem to be out of range. I also put a blank in the middle ("1.00 103.06") to avoid problems with the parser, but to no avail.
Am I doing something wrong here or is this a bug?
Any help on this is greatly appreciated.
Florian
Florian Odronitz wrote: ... > Please note that I used the dope_loopmodel class instead of loopmodel > as indicated in the manual. > When I run the script, it exits with the following message: ... > check_inf__E> Atom 4293 has out-of-range coordinates (usually infinity). > The objective function can thus not be calculated. > > Using dopehr_loopmodel gives the same error whereas the "old" > loopmodel works. > Here is the Atom record from the PDB file: > > ATOM 4293 N LEU 535 10.568 18.659 81.951 1.00103.06 1SG4294 > > The coordinates do not seem to be out of range. I also put a blank in > the middle ("1.00 103.06") to avoid problems with the parser, but to > no avail.
The error refers to the current set of coordinates (during optimization) - not the initial PDB coordinates. And don't put a blank into the PDB file - PDB files are fixed-column format, so it doesn't matter that there's no space between 1.00 and 103.06 (in fact, your "fixed" PDB file is now invalid).
An atomic coordinate at infinity is usually a symptom of large forces in your system. These can occur if you have a bad initial model (e.g. two atoms superposed or very close). It is more likely to occur with DOPE loop modeling than regular loop modeling since the former includes GB/SA. (The loop modeling potentials themselves, while they are atomistic pair potentials, plateau as r tends to 0, unlike electrostatic potentials which tend to infinity.)
> Am I doing something wrong here or is this a bug?
Could be either. You can try a different initial model if your initial model is very bad. Otherwise, send me your input files and I'll try to reproduce your problem, to determine whether it's a bug in the GB/SA code.
Ben Webb, Modeller Caretaker
Hi, I encounter this error too ... It works on my Debian Linux x86, but it fails on my Fedora Linux x86_64 .
I don't know why ..
Yun
On 2008年3月18日 星期二, Modeller Caretaker wrote: > Florian Odronitz wrote: > ... > > > Please note that I used the dope_loopmodel class instead of loopmodel > > as indicated in the manual. > > When I run the script, it exits with the following message: > > ... > > > check_inf__E> Atom 4293 has out-of-range coordinates (usually infinity). > > The objective function can thus not be calculated. > > > > Using dopehr_loopmodel gives the same error whereas the "old" > > loopmodel works. > > Here is the Atom record from the PDB file: > > > > ATOM 4293 N LEU 535 10.568 18.659 81.951 1.00103.06 1SG4294 > > > > The coordinates do not seem to be out of range. I also put a blank in > > the middle ("1.00 103.06") to avoid problems with the parser, but to > > no avail. > > The error refers to the current set of coordinates (during optimization) > - not the initial PDB coordinates. And don't put a blank into the PDB > file - PDB files are fixed-column format, so it doesn't matter that > there's no space between 1.00 and 103.06 (in fact, your "fixed" PDB file > is now invalid). > > An atomic coordinate at infinity is usually a symptom of large forces in > your system. These can occur if you have a bad initial model (e.g. two > atoms superposed or very close). It is more likely to occur with DOPE > loop modeling than regular loop modeling since the former includes > GB/SA. (The loop modeling potentials themselves, while they are > atomistic pair potentials, plateau as r tends to 0, unlike electrostatic > potentials which tend to infinity.) > > > Am I doing something wrong here or is this a bug? > > Could be either. You can try a different initial model if your initial > model is very bad. Otherwise, send me your input files and I'll try to > reproduce your problem, to determine whether it's a bug in the GB/SA code. > > Ben Webb, Modeller Caretaker
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Florian Odronitz -
Modeller Caretaker -
Yun He