Subject: [modeller_usage] [ help ] exceeded maxmol_pdf?
From: "Cathy Chang" <>
Date: Thu, 27 Jul 2006 11:07:24 +0900
Hi,
I'm trying to model a
protein that is about 890 aa long. I was provided with 1NW1 to model against;
however, the problem I ran into was that the output structure from Modeller had
a protein core and a long tail region. I ran my target in 123D+ and found 1JQI
to align fairly well with this trailing tail region, so I want to model my
target with both 1NW1 (core region - 32:A:426:A) and 1JQI (trailing tail
region - 4:A:387:A).
However, when I run
Modeller, I get all of the output except the PDB file, and this error message
keeps appearing in my log file:
>> Summary of
failed models: acad10.B99990001.pdb Obj. func.
(164592.781) exceeded max_molpdf (100000.000) ==> (note: the obj. func. value
changes but it's always over the max)
I tried changing the
domains of both 1NW1 and 1JQI, but I still get the same error message. How would
I be able to avoid exceeding the max pdf size if I want to model my target
with both of the listed proteins against the specific areas of my
target?