Re: Modeller: too many parameters?
Also, if you are using more than 1 templae, it could be that they are aligned such that equivalent distances in the templates are more than say 5 angstroms different. Check the output of CHECK_ALIGNMENT in the log file please. If this is so, that would also increase the number of parameters needed for the splined restraints (fixed dx).
Andrej
szia@hanga.enzim.hu wrote: > > Hi, > > > Please try > > > > SET SPLINE_ON_SITE = off > > > > before CALL ROUTINE = 'model'. > > Thanks. The program seems to be running now, apart from the fact that it > writes some hundreds of thousands of warnings of the following type to the > log file: > > chkder___W> DVY(i) out of bounds: 6646 6646 0.1013E+13 > > But Andras Fiser was here the day before yesterday and he told me that > this is not an actual problem. > > > Can I put this onto the MODELLER usage mailing list? > > Yes, of course. > > Best, > Andras > > Andras Szilagyi (szia@enzim.hu) > 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 sali@rockvax.rockefeller.edu; http://salilab.org
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 (szia@enzim.hu) Institute of Enzymology, Hungarian Academy of Sciences Karolina ut 29., H-1113 Budapest, HUNGARY Fax: +36 1 166 5465, phone: +36 1 166 5633
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
szia@hanga.enzim.hu 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 (szia@enzim.hu) > 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 sali@rockvax.rockefeller.edu; http://salilab.org
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