Re: [modeller_usage] SOLVED headache with alignment

[Francesco Pietra <>]

That was the procedure that I followed.
thanks
francesco


On Tue, Jul 2, 2013 at 8:41 PM, flavio seixas <> 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 <>
> To: 
> 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 <>
> Date: Sun, Jun 30, 2013 at 11:51 AM
> Subject: Fwd: headache with alignment
> To: 
>
>
> 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 <>
> Date: Sun, Jun 30, 2013 at 8:12 AM
> Subject: Fwd: headache with alignment
> To: 
>
>
> 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
> 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
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