I would be surprised if you get a reasonable model even if the symptom
(messages) is cured. Perhaps try a different alignment, different
templates, different RAND_SEED (to get a different starting model).
However, if you really want to cure the symptom: These warnings
fortunately go to standard output so you could edit the mod4 script in
$MODINSTALL/bin/mod4 from
/usr/local/bin/modeller4/bin/${EXECUTABLE} $STEERF > $LOGF
to
/usr/local/bin/modeller4/bin/${EXECUTABLE} $STEERF | grep -v
'chkder___W' > $LOGF
I hope this helps.
Best, Andrej
wrote:
>
> Hi,
>
> My log file from modeller is full of messages like these ones:
>
> chkder___W> DVX(i) out of bounds: 1742 1742Infinity
> chkder___W> DVX(i) out of bounds: 1743 1743Infinity
> chkder___W> DVY(i) out of bounds: 1744 1744Infinity
>
> The log file grows extremely fast. I stopped the program when the log file
> was 182 megabytes big.
>
> With a smaller protein, these warnings do not appear. What could be wrong?
> How can I switch off these warnings, possibly not interfering with other
> warnings?
>
> Best,
>
> Andras Szilagyi ()
> Institute of Enzymology, Hungarian Academy of Sciences
> Karolina ut 29., H-1113 Budapest, HUNGARY
> Fax: +36 1 166 5465, phone: +36 1 166 5633
--
Andrej Sali, Assistant Professor
The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399
tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540
e-mail ; http://salilab.org