Re: [modeller_usage] problem in generating models

[Nupur Bansal <>]

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 <">> 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>