[modeller_usage] Fwd: headache with alignment

[Francesco Pietra <>]

Removing all dots for heatm, and commenting out "env.io.hetatm = True"
no error messages. Actually, both a chloride ion and water molecules
follow, in that order, the aa on the PDB file.
fp


---------- Forwarded message ----------
From: Francesco Pietra <>
Date: Sun, Jun 30, 2013 at 7:28 AM
Subject: Fwd: headache with alignment
To: 


I forgot to mention that the error message of my previous post is
misleading. The F to F matching at chainB F189 is perfect. The cause
why V is seen in place of F should be looked for elsewhere. I retried
by avoiding gaps between the three subunits (see please attachment),
with same error message.

Thanks for advice
francesco pietra



---------- Forwarded message ----------
From: Francesco Pietra <>
Date: Sat, Jun 29, 2013 at 6:58 PM
Subject: headache with alignment
To: 


Hello:
Could a nice person help correcting the mismatch described by mod9.11
for missing residues with a trimer?

read_te_291E> Sequence difference between alignment and  pdb :
                  x  (mismatch at alignment position    551)
 Alignment   .....VVWALCFMGSLALLALVCTNRIQYYFLYPHVTKLDEVAATRLTFPAVTFCNLNEFR
       PDB   DFKVVFTRYGKCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEA
     Match   *****           *
  Alignment residue type   18 (V, VAL) does not match pdb
  residue type    5 (F, PHE),
  for align code XYZ_pure (atom file XYZ_pure), pdb residue number
"189", chain "B"


alignment.ali:

>P1;XYZ0_pure
structureX:XYZ_pure:  50 :A:+1221:C:::-1.00:-1.00
------------------------------------CFMGSLALLALVCTNRIQYYFLYP
HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE
KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG
KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ
DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC
ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK
ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD
IGGQMGLFIGASILTVLELFD---------..............................
............................................................
......................................................./
-------------------------------VVWALCFMGSLALLALVCTNRIQYYFLYP
HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE
KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG
KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ
DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC
ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK
ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD
IGGQMGLFIGASILTVL-------------..............................
............................................................
......................................................./
----------------------------LKRVVWALCFMGSLALLALVCTNRIQYYFLYP
HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE
KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG
KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ
DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC
ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK
ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD
IGGQMGLFIGASILTVLE------------..............................
............................................................
.......................................................
*


>P1; XYZ_pure_fill
sequence:::::::::
GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP
HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE
KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG
KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ
DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC
ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK
ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD
IGGQMGLFIGASILTVLELFDYAYEVIKHR..............................
............................................................
......................................................./
GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP
HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE
KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG
KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ
DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC
ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK
ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD
IGGQMGLFIGASILTVLELFDYAYEVIKHR..............................
............................................................
......................................................./
GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP
HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE
KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG
KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ
DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC
ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK
ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD
IGGQMGLFIGASILTVLELFDYAYEVIKHR..............................
............................................................
.......................................................
*


As the pasted alignment.ali is misreproduced here, even with plain
text, the file is also attached. Dots stand for chloride ions and
water.

Thanks a lot
francesco pietra