How to avoid funny structure in all-hydrogen modeling?
Dear all, Have anyone ever generated all-hydrogen models? For all-hydrogen modeling, the generated models always have some funny structures(such as one hydrogen atom is connected with several other atoms. I think some maybe due to bad contact, but some bond lengths are longer than 2.5 angstrom). These funny connections sometimes appear in ARG and SER. Is it possible because models have not been thoroughly refined? I have tried to set MODELLER "MD_LEVEL" to "refine_1" (# very thorough MD optimization), but no effects. How to avoid or remove these funny structures in all-hydrogen modeling? Thank you very much for your kind help! With best regards, Kong Lesheng
refine_5 is the most extensive MD optimization, not refine_1 ;-)
Bozidar
On Wed, 21 Aug 2002, Lesheng Kong wrote:
> Dear all, > Have anyone ever generated all-hydrogen models? > For all-hydrogen modeling, the generated models always have some funny > structures(such as one hydrogen atom is connected with several other atoms. I > think some maybe due to bad contact, but some bond lengths are longer than > 2.5 angstrom). These funny connections sometimes appear in ARG and SER. > Is it possible because models have not been thoroughly refined? I have tried > to set MODELLER "MD_LEVEL" to "refine_1" (# very thorough MD optimization), > but no effects. > How to avoid or remove these funny structures in all-hydrogen modeling? > Thank you very much for your kind help! > With best regards, > Kong Lesheng >
hello fellow modellers.... im trying to automate modeller to model some 200 proteins. i could generate a script which selects the the group of template. and my compare.top compares all these templates and produces the output file called compare.log.
BUT I DONT know what criteria i should use to select the best template out of the bunch. i attached my
compare.top compare.log files with this mail.(as compar.tar) ..can any one help me ......... what information i should look in LOG file to select best template(s). if it is dendrogram..... how to do it...
many thanx in advance gowtham graduate student ICGEB New Delhi INDIA
Hi Gowtham,
SEQUENCE_SEARCH command will produce output, e.g.:
# CODE_1 CODE_2 LEN1 LEN2 NID %ID %ID SCORE SIGNI SIGNI2 SIGNI3 ---------------------------------------------------------------------------- ---- 1 TvLDH 1bdmA 335 318 153 45.7 48.1 212557. 28.9 -999.0 -999.0 2 TvLDH 1lldA 335 313 103 30.7 32.9 183190. 10.1 -999.0 -999.0 3 TvLDH 1ceqA 335 304 95 28.4 31.3 179636. 9.2 -999.0 -999.0 4 TvLDH 2hlpA 335 303 86 25.7 28.4 177791. 8.9 -999.0 -999.0 5 TvLDH 1ldnA 335 316 91 27.2 28.8 180669. 7.4 -999.0 -999.0
Which you can use to select the best template. More info can be found in manual and in three tutorials on MODELLER web site, under User Manual pages...
Good luck, Bozidar
> hello fellow modellers.... > im trying to automate modeller to model some 200 proteins. i could generate a > script which selects the the group of template. and my compare.top compares > all > these templates and produces the output file called compare.log. > > BUT I DONT know what criteria i should use to select the best template out of > the > bunch. i attached my > > compare.top > compare.log > files with this mail.(as compar.tar) ..can any one help me ......... what > information i should look in LOG file to select best template(s). if it is > dendrogram..... how to do it... > > many thanx in advance > gowtham > graduate student > ICGEB > New Delhi > INDIA >
Hello Gowtham,
you may want to consult one of the many recent reviews from Sali or the following paper from Sanzhez and Sali http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&...
Andras
gowthaman ramasamy wrote: > > hello fellow modellers.... > im trying to automate modeller to model some 200 proteins. i could generate a > script which selects the the group of template. and my compare.top compares all > these templates and produces the output file called compare.log. > > BUT I DONT know what criteria i should use to select the best template out of the > bunch. i attached my > > compare.top > compare.log > files with this mail.(as compar.tar) ..can any one help me ......... what > information i should look in LOG file to select best template(s). if it is > dendrogram..... how to do it... > > many thanx in advance > gowtham > graduate student > ICGEB > New Delhi > INDIA > > ------------------------------------------------------------------------ > Name: compar.tar > compar.tar Type: Unix Tape Archive (application/x-tar) > Encoding: base64
participants (4)
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Andras Fiser -
Bozidar Yerkovich -
gowthaman ramasamy -
Lesheng Kong