That was the procedure that I followed. thanks francesco

On Tue, Jul 2, 2013 at 8:41 PM, flavio seixas oivalf_nix@yahoo.com wrote: > Hi, > It is just a suggestion. > Usualy the pdb file list the protein residues first, followed by the > hetatoms. > Try to edit the pdb file of your template, placing chloride ions coordinates > after the last residue of each protein chain and renumber the chloride > residues to be sequential. > I had a similar problem and it works to me. > Good lucky. > > Flavio > > ________________________________ > From: Francesco Pietra chiendarret@gmail.com > To: modeller_usage@salilab.org > Sent: Tuesday, July 2, 2013 3:06 PM > Subject: [modeller_usage] SOLVED headache with alignment > > 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 > NILVLDIFFEALNYETIEQKKAYEVAGLLGDIGGQMGLFIG ASILTVL------------ > -./----------------------------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 > NILVLDIFFEALNYETIEQKKAYEVAGLLG DIGGQMGLFIGASILTVLELFDYAYEVIKH > 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 > DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSE FYDTYSITACRIDC > 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 > DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWG DCKATTGDSEFYDTYSITACRIDC > 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 > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >