membrane modeling error

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membrane modeling error
#1

Dear everyone,

recently ,I tried to model a structure of a membrane protein.

Do the following script, I created a template.However, the result seems does not reasonable.

${mainpath}/scripts/createTemplate.pl -zonesfile domain1.zone -fastafile${target}/t000_.fasta -parentpdb renum.pdb -outpdb domain1.pdb

for the S4 segement not match the parentpdb.

The alignment file was as this:

Q_domain1/1-289 ILVHSLFNMLIMCTILTNCVFMAQHDPPPWTKYVEYTFTAIYTFESLVKILARGFCLHAF
parent IVESSFFTKFIIYLIVLNGITMGLETSKVYTTLFNQIVITIFTIEIILRIYVHRI-----

Q_domain1/1-289 TFLRDPWNWLDFSVIIMAYTTEFVDLGNVSALRTFRVLRALKTISVISGLKTIVGALIQS
parent SFFKDPWSLFDFFVVAISLVPTSSG---FEILRVLRVLRLFRLVTAVPQMRKIVSALISV

parent IPGMLSVIALMTLFFYIFAIMATQLFGERFP-----------------------------

Q_domain1/1-289 YLSDPENYLLKNGTSDVLLCGNSSDAGTCPEGYRCLKAGENPDHGYTSFDSFAWAFLALF
parent ----------------------------------------------EWFGTLGESFYTLF

Q_domain1/1-289 RLMTQDCWERLYQQTLRSAGKIYMIFFMLVIFLGSFYLVNLILAVVAMA
parent QVMTLESWSGIVRPLME-VYPYAWVFFIPFIFVVTFVMINLVVAICVDA

The parenetpdb and the modeled template pdb file was attached. please ceck.

Even more strangely, by using the same sequence alignment file, the S4 segment in modeled structures that were got from swiss-model. I-TASSER and modeller were all has the right position. I don't think the precision of Rosetta_membrane is lower than that of the three online server. Am I right?

Thanks and best regard!!!

Sincerely, Xiaofeng Ji

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Post Situation:
Mon, 2013-07-01 17:59
benniu2004

I've never used any of these parts of Rosetta, so I can't really answer the question well. I'm not sure I understand the problem. I assume "domain1.pdb" is the same as "template.txt". It looks like a useable template...same coordinates as the reference structure, except at insertions, which have coordinates of 0,0,0. Did it fail somehow when you gave it to the Rosetta membrane modeling executable?

Sun, 2013-09-22 13:48
smlewis