February 2006 - modeller_usage

(no subject)
by Anna Kaczynska 07 Feb '06

07 Feb '06

Hi, I am trying to find out what I should apply in order to receive a protein structure with the lowest objective function of protein structure. Please, can you let me know is you will have any suggestions. Thank you Anna -- Anna Kaczynska (917)834-2291 (cell)

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dna modelling
by rathankar rao 06 Feb '06

06 Feb '06

hi all i need an important information on modelling. i have tried modelling protein sequences but now that i would like to know whether dna could also be modelled using modeller and if yes how can it be done. are there any new files which i have to download or import it from the package itself. plz reply. with regards rathankar --------------------------------- Relax. Yahoo! Mail virus scanning helps detect nasty viruses!

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Help!
by jo hanna 06 Feb '06

06 Feb '06

Hello Sorry for the vast number of posts recently, I think I have finally figured out most of problems. My main question, which I am desperate for suggestions to, is how to read in an existing pdb (x-ray crystal structure) and add the missing residue atoms and the loop region, with minimal disruption to the existing sidechains and backbone. I appreciate that when adding sidechains there will need to be some movement of surrrounding sidechains but I am seeing quite a lot of movement all over my model. I guess however this is possibly because some of the sidechains are actually within quite closely packed regions. I have tried to just refine the loop region and the missing sidechains. and then loop model the missing loop. this works fine for the loop region but the missing sidechain atoms are added with no refinement at all and clash with other added atoms and exiisting sidechains. I have also tried the following script: # Homology modelling by the automodel class from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' a = loopmodel(env, alnfile = 'phe-1phe.ali', # alignment filename knowns = '1phe', # codes of the templates sequence = 'Phe') # 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.md_level = None # No refinement of model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 50 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() # do homology modelling which adds the sidechains, optimises them, adds the loop and then optimises that via the loop modelling routine. However this moves all the other atoms also. Could someone please give me some advice, it would be much apprecaited! J

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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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