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