I checked that the format I used for hetatm is allowed. However, I could not obtain the chloride ion at each subunit. Therefore, I went on with the multimer generated by modeller and placed "manually" the chloride ions in accordance with the crystal structure. fp

---------- Forwarded message ---------- From: Francesco Pietra chiendarret@gmail.com Date: Sun, Jun 30, 2013 at 11:51 AM Subject: Fwd: headache with alignment To: modeller_usage@salilab.org

I have further simplified, first using "w" for water and setting true for w, then removing all water molecules, leaving, as hetatm, only one chloride ion per chain, with alignment.ali that reads

>P1;4FZ0_pure structureX:4FZ0_pure: 50 :A:+1221:C:::-1.00:-1.00 ------------------------------------CFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLELFD---------./----------------------------- --VVWALCFMGSLALLALVCTNRIQYYFLYPHVTKLDEVAATRLTFPAVTFCNLNEFRFS RVTKNDLYHAGELLALLNNRYEIPDTQTADEKQLEILQDKANFRNFKPKPFNMLEFYDRA GHDIREMLLSCFFRGEQCSPEDFKVVFTRYGKCYTFNAGQDGKPRLITMKGGTGNGLEIM LDIQQDEYLPVWGETDETSFEAGIKVQIHSQDEPPLIDQLGFGVAPGFQTFVSCQEQRLI YLPPPWGDCKATTGDSEFYDTYSITACRIDCETRYLVENCNCRMVHMPGDAPYCTPEQYK ECADPALDFLVEKDNEYCVCEMPCNVTRYGKELSMVKIPSKASAKYLAKKYNKSEQYIGE NILVLDIFFEALNYETIEQKKAYEVAGLLGDIGGQMGLFIGASILTVL------------ -./----------------------------LKRVVWALCFMGSLALLALVCTNRIQYYFL YPHVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTA DEKQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTR YGKCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIH SQDEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRI DCETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRY GKELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLL GDIGGQMGLFIGASILTVLE------------.*

>P1; 4FZ0_pure_fill sequence::::::::: GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLELFDYAYEVIKHR./GQPVSIQAFASSSTLHGISHIFSYERLSL KRVVWALCFMGSLALLALVCTNRIQYYFLYPHVTKLDEVAATRLTFPAVTFCNLNEFRFS RVTKNDLYHAGELLALLNNRYEIPDTQTADEKQLEILQDKANFRNFKPKPFNMLEFYDRA GHDIREMLLSCFFRGEQCSPEDFKVVFTRYGKCYTFNAGQDGKPRLITMKGGTGNGLEIM LDIQQDEYLPVWGETDETSFEAGIKVQIHSQDEPPLIDQLGFGVAPGFQTFVSCQEQRLI YLPPPWGDCKATTGDSEFYDTYSITACRIDCETRYLVENCNCRMVHMPGDAPYCTPEQYK ECADPALDFLVEKDNEYCVCEMPCNVTRYGKELSMVKIPSKASAKYLAKKYNKSEQYIGE NILVLDIFFEALNYETIEQKKAYEVAGLLGDIGGQMGLFIGASILTVLELFDYAYEVIKH R./GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFL YPHVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTA DEKQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTR YGKCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIH SQDEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRI DCETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRY GKELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLL GDIGGQMGLFIGASILTVLELFDYAYEVIKHR.*

The error message is that three resids more in the sequence than in the pdb. It deals of the three chlorides. Is that allowed, as I did, to set "." for hetatm after "-" for missing amino acids/ It seems to be incorrect.

thanks francesco pietra

---------- Forwarded message ---------- From: Francesco Pietra chiendarret@gmail.com Date: Sun, Jun 30, 2013 at 8:12 AM Subject: Fwd: headache with alignment To: modeller_usage@salilab.org

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 chiendarret@gmail.com Date: Sun, Jun 30, 2013 at 7:28 AM Subject: Fwd: headache with alignment To: modeller_usage@salilab.org

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 chiendarret@gmail.com Date: Sat, Jun 29, 2013 at 6:58 PM Subject: headache with alignment To: modeller_usage@salilab.org

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