- modeller_usage - salilab.org

Help!
by jo hanna 05 Feb '06

05 Feb '06

Hi I have added missing loop residues to my existing pdb file using the refining only part of the model method (I want to keep the rest of the coordinates unchanged) and then loop optimisation method to optimise the added residues. During this process atoms missing from other residues within the protein chain are also added. My question is how is this done? I have not found any reference to this in the manual. After these atoms are added do they undergo any energy minimisation? I would really appreciate any help with this question as I am confused why after energy minimising these residues myself in another program and then reanalysing my model with the evaluate_model.py script, the dope score I obtain is significantly worse than for the original model from modeller. Many thanks J

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HELP!! Refine part of model
by Matt wagner 03 Feb '06

03 Feb '06

I am refining a segment of my model using the refine part of model script ( http://salilab.org/modeller/manual/node28.html) Everything works fine, but it creates so many atom clashes that when I do an energy minimization on the structure, that the backbone of my protein snaps. Is there another way to reduce these atom clahses? I also did a test in which I turned on bond interactions, by setting env.edat.nonbonded_sel_atoms = 1; but there are still too many atom clashes. Below is a copy of my script: # Addition of restraints to the default ones from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints # Add some restraints from a file: # rsr.append(file='my_rsrs1.rsr') # Restrain the specified CA-CA distance to 10 angstroms (st. dev.=0.1) # Use a harmonic potential and X-Y distance group. rsr.add(atom_ids=('NZ:12', 'NZ:23'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 11.0, 0.01)) rsr.add(atom_ids=('NZ:40', 'NZ:45'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 9.5, 0.01)) rsr.add(atom_ids=('NZ:88', 'NZ:94'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.4, 0.01)) rsr.add(atom_ids=('NZ:94', 'NZ:96'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.4, 0.01)) rsr.add(atom_ids=('NZ:96', 'NZ:106'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 11.4, 0.01)) rsr.add(atom_ids=('NZ:106', 'NZ:107'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 6.5, 0.01)) rsr.add(atom_ids=('NZ:133', 'NZ:140'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 11.4, 0.01)) rsr.add(atom_ids=('NZ:206', 'NZ:208'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 3.8, 0.01)) rsr.add(atom_ids=('NZ:226', 'NZ:238'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 34.2, 0.01)) rsr.add(atom_ids=('NZ:238', 'NZ:239'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 6.9, 0.01)) rsr.add(atom_ids=('N:1', 'NZ:96'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 11.4, 0.01)) rsr.add(atom_ids=('NZ:23', 'NZ:59'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 7.5, 0.01)) rsr.add(atom_ids=('NZ:94', 'NZ:208'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 4.5, 0.01)) rsr.add(atom_ids=('NZ:96', 'NZ:195'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.3, 0.01)) rsr.add(atom_ids=('NZ:96', 'NZ:208'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 7.2, 0.01)) rsr.add(atom_ids=('NZ:96', 'NZ:226'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 11.4, 0.01)) rsr.add(atom_ids=('NZ:118', 'NZ:140'),restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 11.4, 0.01)) rsr.make(aln, restraint_type='ALPHA', residue_ids=('24', '39'), spline_on_site=False) rsr.make(aln, restraint_type='ALPHA', residue_ids=('48', '82'), spline_on_site=False) rsr.make(aln, restraint_type='ALPHA', residue_ids=('100', '129'), spline_on_site=False) rsr.make(aln, restraint_type='ALPHA', residue_ids=('134', '164'), spline_on_site=False) def select_atoms(self): self.pick_atoms(selection_segment=('87:', '113:'), selection_search='segment', pick_atoms_set=1, res_types='all', atom_types='all', selection_from='all', selection_status='initialize') env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' # selected atoms do not feel the neighborhood env.edat.nonbonded_sel_atoms = 2 a = mymodel(env, alnfile = 'TvLDH-mult.ali', knowns = ('1_86','114_243'), sequence = 'TvLDH') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do homology modelling

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loop modelling DOPE score
by jo hanna 03 Feb '06

03 Feb '06

Hi I have done some loop modelling on an existing model. I am confused as although I have selected the BLmodel with the lowest modeller objective function and this BLmodel also has a lower dope score than that of the original model, when I plot the *.profile output from DOPE, the loop region I have optimised shows a higher energy than it was original model. I am confused by this, have i missed something? Thanks Jo

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Re: [modeller_usage] helix alignment with gap
by Guillaume LETELLIER 02 Feb '06

02 Feb '06

> As a general argument, just because an alignment has more true matches > does not mean that it is correct. There are penalties associated with > those two gaps you introduced that offset the gain from exact residue > matching. Not knowing exactly which sequence you are modeling, I > submitted P11229 (ACM1_HUMAN) to the SUPERFAMILY server and the > alignment come back with no gaps in that region. Take a look at: > > http://www.supfam.org/SUPERFAMILY/cgi-bin/gene.cgi?genome=up;seqid=P11229 > > and follow the "Align" link. Obviously, the same can be done for any > protein for which you know the SwissProt number by simply inserting it > at the end of the link above. Not to get into prolonged argument here, > I'll just say that I would trust SUPERFAMILY-based alignment over any > human-derived alignment unless there is a very good reason to believe > that the server alignment is wrong. And breaking a long helix to make > few extra positive matches usually doesn't qualify as a good reason, > especially because it forces you to make a compensatory two-residue > gap later in the model. But don't take my word for it, try modeling > the protein with and without those gaps and see which model evaluates > better. > > Hope this helps, > > Mensur Here there are strong argument that kinda end the gap debate ... Thanks for preventing me to lost my time and make huge mistakes. (the gapped models came with objective function score at least double of the 'classical' ones) At least have I learned to play with the alpha constraint of modeller ;o) . Regards Guillaume

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helix alignment with gap
by Guillaume LETELLIER 02 Feb '06

02 Feb '06

Hi all I am new to modeller and i'm currently trying to build a model of a GPCR using the bovine rhodopsin structure as template. I have notice that in the middle of one of a region corresponding to a transmembrane segment, there is a very unambiguous gap of two residue in the sequence alignment. Two model of this receptor have already been published and in both cases, authors have used sequence alignment without gaps, which means that half the residues of this TM are clearly not correctly aligned with the template. I am confuse of how I should handle this gap to build my model. Using a 2 residues helix-gapped alignment in modeller would result in a model with - ugly coil in the middle of the helix - a switch from one helix face to the opposite of amino acids - a longer loop next to the TM (or maybe a longer helix ?) On the contrary, ignoring the gap and using a wrong alignment result in a much better looking helix. Should I deliberately ignore the sequence similarity to provide modeller an alignment with no gap in the TM ? Best regards, Guillaume LETELLIER

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building in a loop
by jo hanna 02 Feb '06

02 Feb '06

Hi I have a quick question realting to this post from last October: mathieu coincon wrote: I had a structure where a 15-residues loop is missing. So I want to create it but without moving the other atoms. I tried a lot of things (md_level= None, and so...) but I wasn't able to obtain a model where the non-loop atoms stayed in place. I think that there is still an optimization I can't stop. After that I could try to optimize my loop with the refine_loop.py from the advanced tutorial but first I need my model. >The suggestion you received was nearly right - you should specify 'exit_stage=2' when you call automake.make(). See http://salilab.org/modeller/manual/node52.html >For example, >a = automodel(... >a.make(exit_stage=2) >If you actually want to optimize the loop region, then simply select only the loop residues for optimization. See http://salilab.org/modeller/manual/node28.html for optimization >using the standard potentials, and the second example at http://salilab.org/modeller/manual/node33.html for optimizing using Modeller's loop modeling potential. > Ben Webb, Modeller Caretaker I have tried to add in resdiues missinhjg from a loop in my pdb in two ways; 1. using the exit stage method to build a model with the aurtomodel class (where the resisues are added but in a complete straight line not joined at both ends of the loop) and then loop optimisation to join the added piece to the protein and optimise and 2. By using the loop modelling rotine directly or the refine only a certain section to add in and then loop modelling this section. My question is that the first method preoduces a model with a lower objective function than the second, seemingly regardless of how many models I build. Would someone be able to comment on the validity of method one for building a loop in? Thanks Jo

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fix_offsets to align certain residues
by jf163201＠ohio.edu 30 Jan '06

30 Jan '06

Hi, I'm trying to figure out how to use fix_offsets with align2d. Please follow this example, based on the salign() example (under the 'Alignments using external restraints subsection') in the manual. Here is the input file, fix_positions.ali >P1;1abc sequence:1abc:1::10:: : :-1.00:-1.00 FGAVAFATTT* >P1;1def sequence:1def: :: :: : :-1.00:-1.00 AVAFATTT* >P1;_fix_pos sequence:x: :: :: : :-1.00:-1.00 0000000000* Following is the .py file. I've removed the comments but it's taken directly from the manual log.verbose() env = environ() aln = alignment(env, file='fix_positions.ali', align_codes=('1abc', '1def', '_fix_pos')) aln.salign(fix_offsets=(0, 1000, 2000, 3000, 4000), gap_penalties_2d=(0, 0, 0, 0, 0, 0, 0, 0, 0), # Any values are # possible here local_alignment=False, # Local alignment works, too gap_penalties_1d=(-600, -400)) # This is best with the default value # of gap_penalties_2d aln.write(file='fix_positions_salign.pap', alignment_format='PAP') If I run this, I will get an alignment of: _aln.pos 10 1abc FGAVAFATTT 1def --AVAFATTT _consrvd ******** But suppose I want to force the first Alanine in 1abc to be aligned with the 2nd Alanine in 1def. I want modeller to align all other residues normally (as it normally would without any fix_offsets). So I want something that would _probably_ look like this: _aln.pos 10 1abc FGAVAFATTT 1def AVA--FATTT _consrvd ******** The only thing that matters is that the first A in 1abc is forced to align with the 2nd A in 1def. How do I get these particular Ala residues to be forced to align using _fix_pos input in the alignment file? Specifically, what would I need to put in place of the zeros below? >P1;_fix_pos sequence:x: :: :: : :-1.00:-1.00 0000000000* I've been playing around with it but can't seem to get it work correctly. To ask the question a different way, given two sequnces, A and B, how does one tell Modeller the residue #X of sequence A must be aligned with residue #Y of sequence B. Thank you, Jim Fonseca

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problem with ligand attachment
by Natasha Khan 30 Jan '06

30 Jan '06

Hello I am trying to attach hetatoms*(4 Mn,4 Mg,4 NAD, and 1027 water molecules)* to my model(an enzyme) using mod8v1,but somehow I always fail to get the output files(*B9999?????* *and the V9999???? files *).I do get the other output files*(D00000?????,.ini,.rsr,.sch).* *The error that I get in the log file is:* ** delete__442E> One or more atoms absent from MODEL: O:1976: C:1976: N:1977: CA:1977: delete__442E> One or more atoms absent from MODEL: O:1977: C:1977: N:1978: CA:1978:.................................................................................. ............................................................................................................ ..........................so on. ** *And the other error that it shows*: csrrng__299E> Atom index is out of bounds: 30677 30676 csrrng__299E> Atom index is out of bounds: 30680 30676 nselat__596E> Atom index is out of range (iatm,natm): 30680 30676 SOMEONE PLEASE SUGGEST A SOLUTION FOR WHY THE MODEL IS NOT ACCEPTING THE HETATOMS? Thanks Natasha

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alignment matrix
by Schulze, Diana 30 Jan '06

30 Jan '06

Dear all, I made a model with modeller and used the function auto_align() to get an automatic alignment. Now my question is the following: How can I find out which matrix (BLOSOM 60,...) was used to build this alignment? Sincerely, Diana Schulze

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Unexpected keyword argument
by Eva María Priego 25 Jan '06

25 Jan '06

Dear users, I'm trying to make two strands in my model (Modeller8v0 , Windows) I have search the FAQ and I tried one script found there, but I get this error: a= mymodel (env, alnfile='JP.ali', knows='JAN', 'sequence='B-1') a= mymodel (env, ) mymodel get an unexpected keyword argumen 'alnfile'. I don't know what to do. Can someone help me?. Thank you in advance. Eva Here is my script: #Make two STRANDS def mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints rsr.make(aln, restraint_type='STRAND', residue_ids=('63', '67')) rsr.make(aln, restraint_type='STRAND', residue_ids=('134', '137')) log.verbose() env = environ() env.io.atom_files_directory = '' a.starting_model= 1 a.ending_model = 30 a = mymodel(env, alnfile='JP.ali', knowns='JAN', sequence='B-1') a.make()

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