I'm trying run align2d on 3dxn chain a's pdb and it's sequence provided by the pdb.
My code is as below:
from modeller import *
env = environ()
aln = alignment(env)
mdl = model(env, file="3dxn_nmin")
aln.append_model(mdl, align_codes='structure', atom_files="3dxn_nmin.pdb")
aln_block = len(aln)
aln.append('3dxn.a.fasta', alignment_format='FASTA')
aln.align2d(align_block=aln_block, output_weights_file='2dalign.mtx')
aln.check_sequence_structure()
aln.write(file='tmp.ali', alignment_format='PIR')
In the alignment, I get:
>P1;structure
structureX:3dxn_nmin.pdb: 19 :A:+258 :A:::-1.00:-1.00
------------------LSDRYQRVKKLG--SYGEVLLCKDK-TGAERAIKIIKKSSVTTTSNSGALLDEVAVL
KQLDHPNIMKLYEFFEDKRNYYLVMEVYRGGELFDEIILRQKFSEVDAAVIMKQVLSGTTYLHKHNIVHRDLKPE
NLLLESKS-DALIKIVDFGLSAHFE-------RLGTAYYIAPEVLRKKYDEKCDVWSCGVILYILLCGYPPFGGQ
TDQEILKRVEKGKFSFDPPDWTQVSDEAKQLVKLMLTYEPSKRISAEEALNHPWIVKFCSQK*
>P1;3DXN:A:sequence
sequence:: : : : :::-1.00:-1.00
MHHHHHHSSGRENLYFQGLSDRYQRVKKLGSGAYGEVLLCKDKLTGAERAIKIIKKSSVTTTSNSGALLDEVAVL
KQLDHPNIMKLYEFFEDKRNYYLVMEVYRGGELFDEIILRQKFSEVDAAVIMKQVLSGTTYLHKHNIVHRDLKPE
NLLLESKSRDALIKIVDFGLSAHFEVGGKMKERLGTAYYIAPEVLRKKYDEKCDVWSCGVILYILLCGYPPFGGQ
TDQEILKRVEKGKFSFDPPDWTQVSDEAKQLVKLMLTYEPSKRISAEEALNHPWIVKFCSQK*
If
you look at the biggest gap, preceded by "HFE" in the alignment, that E
should be at the other end of the gap. Sequence-wise, having it at
either end is equivalent (there is an E in both places), but the actual pdb file has "ERL" at the other end and "HF" preceding.
When I run the check_sequence_structure(), it agrees, saying:
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
174 1 174 182 F E 12.004
END OF TABLE
I've placed the files at github if they are of any help
They can be cloned at:
git clone git://gist.github.com/114942.git
Thanks,
David