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>