July 2013 - modeller_usage

Select and remove atoms from automodel
by Ignacio Ibarra 04 Mar '14

04 Mar '14

Hello, Currently I am generating nucleic acid models using the MODELLER suite. I would like to remove the initial phosphate group declared in the first residue of each nucleic acid chain. Those atoms should not be present in real structures. I would like to do it without writing new text in the .lib files that are into the modlib folder I read about a pick_atoms() method in an older version of MODELLER, but it is not commented in the 9v11 manual ( http://binf.gmu.edu/software/MODELLER/… [View More]

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Make non-adjacent mutations, preserve backbone and avoid clashes
by David Johnson 30 Jul '13

30 Jul '13

I would like to make a handful of mutations that are not necessarily in sequential order in the primary structure. I would like to preserve the backbone of the model and to keep fixed all side-chains except those of the mutations and possibly nearby residues, which are to be moved ONLY if necessary to void steric clashes. Thus far I have tried Selecting all but the mutated atoms and setting env.edat.nonbonded_sel_atoms = 2 a.library_schedule = autosched.slow a.md_level = None OR a.… [View More]

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Build missing residues for multisubunit protein
by Kelly Tran 29 Jul '13

29 Jul '13

Hi, Do you have suggestions on how to build missing residues for a multisubunit protein while restricting non-missing residues from moving? --- from modeller import *from modeller.automodel import * # Load the automodel classlog.verbose()env = environ()# directories for input atom filesenv.io.atom_files_directory = ['.', '../atom_files'] class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('1', '1'), self.residue_range('1', '2'), self.residue_range('181','… [View More]

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Ligand Introduction from non-homologous protein
by Rohitesh Gupta 16 Jul '13

16 Jul '13

Dear Team, I am writing this mail again. Not sure, if my earlier mail was received by the group. I am trying to model a protein using a template that is 85% similar to it, but also wants to transfer ligand from another protein that is 10% similar. In doing so, I am introducing restraints while creating the final model with ligand. But the final output as .pdb, the ligand seems to miss all the restraints that is being introduced. Please find herein the code: from modeller import * … [View More]

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Modeling Ligand from non-homologous protein
by Rohitesh Gupta 16 Jul '13

16 Jul '13

Hello everyone, I have a query which is similar to the process followed in transferring ligand from non-homologous protein under the advanced modelling section on the website. To obtain the restraints on pyruvate, we first superpose the structures of several LDH and MDH enzymes solved with ligands. Such a comparison allows us to identify absolutely conserved electrostatic interactions involving catalytic residues Arg161 and His186 on one hand, and the oxo groups of the lactate and malate … [View More]

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making ideal alpha-helix
by Jan Kosinski 12 Jul '13

12 Jul '13

Dear all, I am having a trouble with making an alpha helix example ( http://salilab.org/modeller/wiki/Make%20alpha%20helix) It works fine for shorter helices, but if I increase helix length and do e.g. m.build_sequence('AAAAAAAAAAAAAAAAAA') then the resulting helix is far from perfect, has local distortions and largely is not recognized as helix by DSSP (it shows mixed H and T conformation), and not drawn as helical cartoon in pymol. The situation does not improve if I increase the … [View More]

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multiple templates alignment with target
by Ramin Ekhteiari 05 Jul '13

05 Jul '13

Hi, Would you please let me know, by which python script can I align multiple templates with my target? Cheers,

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Preserving orientation of structure
by Thomas Albers 05 Jul '13

05 Jul '13

Hello! I would like to model a poorly resolved loop in a crystal structure on another crystal structure where that loop is better resolved. This is easy to do, however, this loop has coordinates that fit the target structure. Is there a way to tell Modeller to fit the source, so I won't have to reorient that loop after? Thomas

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Re: [modeller_usage] SOLVED headache with alignment
by Francesco Pietra 02 Jul '13

02 Jul '13

That was the procedure that I followed. thanks francesco On Tue, Jul 2, 2013 at 8:41 PM, flavio seixas <oivalf_nix(a)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 … [View More]works to me. > Good lucky. > > Flavio > > ________________________________ > From: Francesco Pietra <chiendarret(a)gmail.com> > To: modeller_usage(a)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(a)gmail.com> > Date: Sun, Jun 30, 2013 at 11:51 AM > Subject: Fwd: headache with alignment > To: modeller_usage(a)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(a)gmail.com> > Date: Sun, Jun 30, 2013 at 8:12 AM > Subject: Fwd: headache with alignment > To: modeller_usage(a)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(a)gmail.com> > Date: Sun, Jun 30, 2013 at 7:28 AM > Subject: Fwd: headache with alignment > To: modeller_usage(a)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(a)gmail.com> > Date: Sat, Jun 29, 2013 at 6:58 PM > Subject: headache with alignment > To: modeller_usage(a)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(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > > [View Less]

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SOLVED headache with alignment
by Francesco Pietra 02 Jul '13

02 Jul '13

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(a)gmail.com> Date: Sun, Jun 30, 2013 at 11:51 AM Subject: Fwd: headache with alignment To: modeller_usage(a)salilab.org I have further simplified, … [View More]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(a)gmail.com> Date: Sun, Jun 30, 2013 at 8:12 AM Subject: Fwd: headache with alignment To: modeller_usage(a)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(a)gmail.com> Date: Sun, Jun 30, 2013 at 7:28 AM Subject: Fwd: headache with alignment To: modeller_usage(a)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(a)gmail.com> Date: Sat, Jun 29, 2013 at 6:58 PM Subject: headache with alignment To: modeller_usage(a)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 [View Less]

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