Organization: Dept. of Microbiology & Molecular genetics; STAFFORD HALL; Univ. of Vermont.
Hi,
I have this problem solved. I had a wrong representation of the Zn
heteroatoms in my PDB file. It had to be annotated as ZN2 and not ZN,
because that's how it's represented in the top_heav.lib file.
Thanks to one of the modeller users who pointed this out to me - I'm
sorry I forget his name.
Regards,
Sirisha Sunkara
--- Begin Message ---
To: ,
Subject: Problems with heteroatoms (Zn)
From: Sirisha sunkara <>
Date: Fri, 17 Aug 2001 13:12:47 -0400
Organization: Dept. of Microbiology & Molecular genetics; STAFFORD HALL; Univ. of Vermont.
Hi,
I'm trying to model a 283 aa long protein using Modeller4 with Zn
heteroatom. The problem is Zn heteroatom does not show up in my output
file. My template structure has a Zn Heteroatom in it. At this point I'm
not interested in a model with hydrogens or water.
I know people have had similar problems earlier and I also tried all
the methods suggested in the archives of the mailing lists from 1998 and
1999. It still doesn't work. Has there been any update in the library
files in Modeller5 for this?
My model-segment.top file looks like this:
INCLUDE # Include the predefined TOP
routines
SET ALNFILE = 'file.ali'
SET KNOWNS = 'abc'
SET SEQUENCE = 'gi_xxxxxxxx'
SET ATOM_FILES_DIRECTORY = './:../atomfiles'
SET TOPOLOGY_MODEL =3, HYDROGEN_IO = off, WATER_IO = off, HETATM_IO = on
READ_PARAMETERS FILE = '$(LIB)/par.lib'
READ_TOPOLOGY FILE= '$(LIB)/top_heav.lib'
SET STARTING_MODEL= 4
SET ENDING_MODEL = 4
SET DYNAMIC_FLAG = 0
CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'select_atoms'
PICK_ATOMS SELECTION_SEGMENT='1:' '283:', SELECTION_SEARCH='segment', ;
PICK_ATOMS_SET=1, RES_TYPES='all', ATOM_TYPES='all', ;
SELECTION_FROM='all', SELECTION_STATUS='initialize', SELECTION_STEP=1
RETURN
END_SUBROUTINE
I have Zn in my alignment files set up as XXX/z* in both template and
query sequences. My template PDB file also has "only ZN" heteroatoms - I
stripped out all other heteroatoms in my template PDB file just to make
sure.
What am I doing wrong?
I appreciate all your help,
Sirisha Sunkara