Dear Modeller users!
I've followed 1st modeller tutorial making alignment of my target against 1 template (with the inclusion of hetatm from the template). As the result I've obtained the below alignment
>P1;2rh1A structureX:2rh1.pdb: 29 :A:+283 :A:::-1.00:-1.00 ---------DEVWVVGMGIVMS----------LIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGL AVVPFGAAHILMKMWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWI VSGLTSFLPIQ-MH--WYRATHQE-----AINCYAEETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEA KRQLKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYC-RSPDF RIAFQELLCL------.*
>P1;od_r sequence:od_r: : : : ::: 0.00: 0.00 MEGKNLTSISECFLLGFSEQLEEQKPLFGSFLFMYLVTVAGNLLIILVIITDTQLHTPMYFFLANLSLADACFVS TTVPKMLANIQIQSQAISYSGCLLQLYFFMLFVMLEAFLLAVMAYDCYVAICHPLHYILIMSPGLCIFLVSASWI MNALHSLLHTLLMNSLSFCANHEIPHFFCDINPLLSLSCTDPFTNELVIFITGGLTGLICVLCLIISYTNVFSTI LKIPSA-QGKRKAFSTCSSHLSVVSLFFGTSFCVDFSSPSTHSAQKDTVASVMYTV--VTPMLNPFIYSLRNQEI KSSLRKLIWVRKIHSP-*
where Od_r is the modeled protein and 2rh1 is the template consisted of ligand ('.' in aliugn file)
now I'm running script for making models (where ligand should be included from the template and obtain error about atom mismatches
from modeller import * from modeller.automodel import *
# Read in HETATM records from template PDBs env.io.hetatm = True env.io.hydrogen= True # directories for input atom files env.io.atom_files_directory = ['.', './results']
env = environ() a = automodel(env, alnfile='result.ali', knowns='2rh1A', sequence='od_r', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 10 a.make()
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 283 282 For alignment entry: 1 2rh1A
how it could be fixed and obtain models with the ligands in the positions identical to the templates ?
James
On 4/15/14, 2:05 AM, James Starlight wrote: > I've followed 1st modeller tutorial making alignment of my target > against 1 template (with the inclusion of hetatm from the template). As > the result I've obtained the below alignment
As pointed out already, you haven't told Modeller to put the ligand in the model. Is it possible that you modified the 2rh1.pdb file? Your template sequence doesn't match the one in 2rh1 from PDB (there's an extra sequence in the official PDB from residue 1002:A to 1161:A that isn't in yours). Maybe you removed the ligand by mistake too.
Ben Webb, Modeller Caretaker
Thanks for suggestions again!
Could you tell me as well 1) what should I provide to the below ali.py script to copy HETATM from the template to the model
env = environ() aln = alignment(env) # Read in HETATM records from template PDBs env.io.hetatm = True env.io.hydrogen= True
mdl = model(env, file='3eml', model_segment=('FIRST:A','LAST:A')) aln.append_model(mdl, align_codes='3emlA', atom_files='3eml.pdb') aln.append(file='od_r.ali', align_codes='od_r') aln.align2d() aln.write(file='result3.ali', alignment_format='PIR') aln.write(file='result3.pap', alignment_format='PAP')
2) how salt bridges can be defined in the model taken from the template with the homology cysteins in the same positions?
James
2014-04-15 23:03 GMT+04:00 Modeller Caretaker modeller-care@salilab.org:
> On 4/15/14, 2:05 AM, James Starlight wrote: > >> I've followed 1st modeller tutorial making alignment of my target >> against 1 template (with the inclusion of hetatm from the template). As >> the result I've obtained the below alignment >> > > As pointed out already, you haven't told Modeller to put the ligand in the > model. Is it possible that you modified the 2rh1.pdb file? Your template > sequence doesn't match the one in 2rh1 from PDB (there's an extra sequence > in the official PDB from residue 1002:A to 1161:A that isn't in yours). > Maybe you removed the ligand by mistake too. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >
On 4/15/14, 11:40 PM, James Starlight wrote: > 1) what should I provide to the below ali.py script to copy HETATM from > the template to the model
This is done in the alignment file.
> 2) how salt bridges can be defined in the model taken from the > template with the homology cysteins in the same positions?
http://salilab.org/modeller/9.13/manual/node24.html
Ben Webb, Modeller Caretaker
Thanks for suggestions again!
regarding S-S bridges I've understood well the method of the manual S-S bond definition using *model.patch() http://salilab.org/modeller/9.13/manual/node182.html#CMD:model.patch*method. On other hand I wounder to know how alternative model.patch_ss_templates() method could be implemented taking S-S from the templates. For instance using modeller advanced tutorial I've obtained results of the multiple-sequence alignment with the inclusion of the aligned sequence + several temples sequences (this output alignment is produced reasonable model). Next I used
* patch_disulfides.py example with this alignment to obtain stereochemical restraints.# Create the disulfide bonds using equivalent disulfide bonds in templates:mdl.patch_ss_templates(aln)# Create the stereochemical restraintssel = selection(mdl)mdl.restraints.make(sel, restraint_type='stereo', spline_on_site=False) Now how I could perform such restrains-guided modelling to build model with the S-S bridges?*
*James*
2014-04-16 23:13 GMT+04:00 Modeller Caretaker modeller-care@salilab.org:
> On 4/15/14, 11:40 PM, James Starlight wrote: > >> 1) what should I provide to the below ali.py script to copy HETATM from >> the template to the model >> > > This is done in the alignment file. > > > 2) how salt bridges can be defined in the model taken from the >> template with the homology cysteins in the same positions? >> > > http://salilab.org/modeller/9.13/manual/node24.html > > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >
On 4/18/14, 12:22 AM, James Starlight wrote: > On other hand I wounder to know how alternative > model.patch_ss_templates() method could be implemented taking S-S from > the templates.
I have no idea what you're asking here, sorry. patch_ss_templates is already implemented (no "could be"), is described in the manual, and is called automatically in the automodel protocol. If you want to call it in your own protocol, what you show looks fine to me.
Ben Webb, Modeller Caretaker
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Modeller Caretaker