- modeller_usage - salilab.org

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 * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints for ids in (('O:234:', 'N4:286:'), ('O:242:', 'N4:286:'), ('N:234:', 'O2:286:')): atoms = [self.atoms[i] for i in ids] rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(*atoms), mean=3.0, stdev=0.2)) log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files # env.io.atom_files_directory = './:../atom_files/' # Read in HETATM records from template PDBs env.io.hetatm = True a = MyModel(env, alnfile = 'alignment.ali', # alignment filename knowns = ('2ebd_model','1ro7'), # codes of the templates sequence = '2ebd') # assess_methods=(assess.DOPE, assess.GA341)) # code of the target a.starting_model= 1 # index of the first model a.ending_model = 5 # index of the last model # (determines how many models to calculate) a.make() This code runs fine but the ligand doesn't have any of the above mentioned restraints. How could one instruct modeller to consider these restraints? I understand that modeller would by default consider the non-bonded interaction between ligand and the catalytic site amino acids. In such case, is there a way to override those interactions? If so, which files should be edited? It will be really helpful to receive suggestions on these lines. Thanking you in anticipation, Rohitesh

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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 ligands on the other hand. The modeling script can now be expanded by creating a new class 'MyModel', which is derived from automodel but which differs in one important respect: the special_restraints routine is redefined to add, to the default restraints, some user defined distance restraints between the conserved atoms of the active site residues and their substrate. In this case, a harmonic upper bound restraint of 3.5±0.1Å is imposed on the distances between the three specified pairs of atoms. A trick is used to prevent MODELLER from automatically calculating distance restraints on the pyruvate-TvLDH complex; the ligand in the 1emd_bs template is moved beyond the upper bound on the ligand-protein distance restraints (i.e., 10). I am unable to understand the process of moving the ligand in 1emd_bs beyond the upper bound? As in, how does one not let modeller choose the default restraints from the template such that the user-defined restraints are considered for modeling ligand into the target protein. Any suggestions on these lines would be very much appreciated. Thanking you in anticipation, Rohitesh

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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 number of conjugate gradient steps. The extent of distortions does seem to be somewhat sequence dependent. Is there a better way of making an ideal alpha helix with Modeller ? I tested on Modeler 9.11 and 9.12. Thanks in advance for help, Jan

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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 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 > >

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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, 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

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automodel/Mymodel
by Ramin Ekhteiari 01 Jul '13

01 Jul '13

Hi, I want to ask a base question, please let me know the main deference between these two python scripts. I suppose the deference is *this*: the first one do the comparative modeling with the base of template for all residues, but the second one, do the same except for residues 197 - 198. But I see a main deference between the results (output structures) are the applied methods of these two script are the same or not? Cheers Ramin #1 env = environ() a = automodel(env, alnfile='Drd2-3SN6.ali', knowns='3SN6', sequence='Drd2', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1000 a.ending_model = 1000 a.make() ----------------------------------------------------------------------------------------- #2 class MyModel(automodel): def select_atoms(self): return selection(self) - selection(self.residue_range('197', '198')) env = environ() a = MyModel(env, alnfile = 'Drd2-3SN6.ali', knowns = '3SN6', sequence = 'Drd2', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model= 1005 a.ending_model = 1005 a.make() ---------------------------------------------------------

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headache with alignment
by Francesco Pietra 30 Jun '13

30 Jun '13

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

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Denovo loop remodeling
by Ramin Ekhteiari 28 Jun '13

28 Jun '13

Hi, Is there any Denovo loop remodeling on the base of the fragment data base in MODELLER? Cheers, Berk

2 3