On Fri, Mar 05, 2004 at 05:57:15PM +0100, Matthias wrote: > I have more then one question, so far: > - How do I use the "user_after_singel_model" subroutine, for ex. to > compare the model with an X-ray > structure? Can you send me a sort of top.script, or at least, can > you someone give me a hint?

You simply define a routine called user_after_single_model, and it will be called immediately before each model is written out to disk. The generated model is available as MODEL, so you can read in MODEL2 from your X-ray structure and do a SUPERPOSE or ALIGN3D or whatever. See for example http://salilab.org/modeller/manual/node91.html

> - Further, can you please check my top.script , please? I can't > undestand why it sometimes doesn't work (.. it clashed more than > once... and it appeared the message: > FORTRAN runtime error: > INQUIRE(UNIT=/usr/bin/mod6v2: line 38: 25355 segmentation fault > (core dumped) $nice ${executable} $STEERF >$LOGF > Can you explain me, what this mean?

Possibly a bug in Modeller - you shouldn't be seeing segmentation faults. Send me your inputs (including PDBs) and I'll see if I can reproduce it here.

> - At last but not least, how can i eliminate the error: "Array too > small. Increase MPAIRS"

This indicates that Modeller's guess at the number of nonbond pairs turned out to be too small. This shouldn't occur unless you are using atoms with unphysical Van der Waals radii, or there is a Modeller bug. Send me a set of inputs which reproduces this problem.

> or "Array too small. Increase MAXATM", > and what's the reason for it?

This can happen at several places in the code - I can't tell what problem you're running into without seeing your input files.

Ben Webb, Modeller Caretaker