Hi,

Thanks for replying. Now, after making that change, I am getting the following error: Alignment sequence not found in PDB file: 1 atom_files/2hzv.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.)

But, I don’t know how to specify the starting and ending residue numbers.

On Jan 29, 2014, at 12:11 PM, Nupur Bansal nupur.b298@gmail.com wrote:

> Hi, > > I am new to Modeller and has been trying to use it for generating models for my system. > > I have done sequence alignment using Clustalw in .pir format. But, the error I am getting is : > check_a_282E> Unable to read structural information for alignment > sequence: 1 2hzv > This command requires structures. > > > My alignment file is : 2ca9_2hzv.ali > > >P1;2hzv > NMR:2hzv.pdb:FIRST:@ END:::::: > --MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQG---FAV > LSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDV > IAQRGVRHGHLQCLP--KEDMQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSAL > AQEATQQHGTQG---FAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLE > IAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLP----KEDMQRVTITLDDDLLETLDSLS > QRRGYNNRSEAIRDILRSALAQEATQQHGTQG---FAVLSYVYEHEKRDLASRIVSTQHH > HHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLP--KEDMQ > RVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQG---FAVLSYV > YEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQR > GVRHGHLQCLPKED--* > > >P1;2CA9_apo > sequence:2CA9_apo:FIRST:@ END:::::: > DSIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAV > LVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEI > GGLRGVKFAKLTKASSFEYSIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKL > VEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLE > TIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFEYNDSIIRFSVSLQQNLLDELDNRI > IKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHA > SGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFEYSII > RFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVI > YDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLR > GVKFAKLTKASSFEYN* > > > I am also attaching my pdb file for reference. > > Any help would be appreciated. > > Thanks, > Nupur > <2hzv.pdb>