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<DIV><SPAN class=080005507-21072006><FONT face=Verdana>Hi,</FONT></SPAN></DIV>
<DIV><SPAN class=080005507-21072006><FONT
face=Verdana></FONT></SPAN> </DIV>
<DIV><SPAN class=080005507-21072006><FONT face=Verdana>My name is Cathy. I'm a
new user of Modeller, and I'm still trying to figure out the input files to run
Modeller. I'm having trouble with the atom files...I don't exactly know what is
an atom file.</FONT></SPAN></DIV>
<DIV><SPAN class=080005507-21072006><FONT
face=Verdana></FONT></SPAN> </DIV>
<DIV><SPAN class=080005507-21072006><SPAN class=080005507-21072006><FONT
face=Verdana>I tried using the .pdb file straight from the PDB. I tried changing
the file content to just the "atom" section of the PDB files. And nothing seems
to work.</FONT></SPAN></SPAN></DIV>
<DIV><SPAN class=080005507-21072006><FONT
face=Verdana></FONT></SPAN> </DIV>
<DIV><SPAN class=080005507-21072006><FONT face=Verdana>I have the script file
& alignment file in the default Modeller directory, and I set the atom file
environment to a folder named "atom_files" with the 2 atom files (1pme &
1wbn). But when I try running my script, it says that atom files cannot be found
in the directory atom_files. Here's the exact error message:</FONT></SPAN></DIV>
<DIV><SPAN class=080005507-21072006><FONT
face=Verdana></FONT></SPAN> </DIV>
<DIV><SPAN class=080005507-21072006><FONT face=Verdana>==========<SPAN
class=080005507-21072006><FONT
face=Verdana>==========</FONT></SPAN></FONT></SPAN></DIV>
<DIV><SPAN class=080005507-21072006><FONT face=Verdana><SPAN
class=080005507-21072006></SPAN></FONT></SPAN> </DIV>
<DIV><SPAN class=080005507-21072006><FONT face=Verdana>Read the alignment from
file : 1pme_1wbn.ali<BR>Total number of
alignment positions: 388</FONT></SPAN></DIV>
<DIV> </DIV>
<DIV><SPAN class=080005507-21072006><FONT face=Verdana> #
Code #_Res #_Segm
PDB_code
Name<BR>-------------------------------------------------------------------------------<BR>
1 1pme
380 1
1pme <BR> 2
1wbn 360
1 1wbn <BR>runcmd______>
alignment.check()</FONT></SPAN></DIV>
<DIV> </DIV>
<DIV><SPAN class=080005507-21072006><FONT face=Verdana>check_a_343_> >>
BEGINNING OF COMMAND<BR>openf5__224_>
Open 11 OLD SEQUENTIAL
\Modeller8v2\atom_files\1pme.atm<BR>rdpdb___303E> No atoms were read from the
specified input PDB file, since
the<BR>
starting residue number and/or chain id in MODEL_SEGMENT
(or<BR>
the alignment file header) was not
found;<BR>
requested starting position: residue number " 0", chain " "<BR>rdabrk__288W>
Protein not accepted: 1
1pme<BR>check_a_337E> Structure not read in (please consult the log
file<BR>
for more details): 1
1pme</FONT></SPAN></DIV>
<DIV><SPAN class=080005507-21072006><FONT face=Verdana><BR><SPAN
class=080005507-21072006><FONT face=Verdana>==========<SPAN
class=080005507-21072006><FONT
face=Verdana>==========</FONT></SPAN></FONT></SPAN><BR></FONT></SPAN><SPAN
class=080005507-21072006><FONT face=Verdana></DIV></FONT></SPAN>
<DIV><SPAN class=080005507-21072006><FONT face=Verdana>It would be great if
anyone can help me with this problem! Thank you very much for your
time!</FONT></SPAN></DIV>
<DIV><SPAN class=080005507-21072006><FONT
face=Verdana></FONT></SPAN> </DIV>
<DIV><SPAN class=080005507-21072006><FONT face=Verdana></FONT></SPAN><SPAN
class=080005507-21072006><FONT face=Verdana>-
Cathy</DIV></FONT></SPAN></BODY></HTML>