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Questions on loop modelling
by hori koshii 16 Jun '06

16 Jun '06

My target sequence has two insertions at 2 loop regions (14aa, 9aa) when compare to my template structure. I have three questions: 1. Since 12aa is the limit of loop modelling, is that viable to build a "model" with the "template sequence plus 2 aa of the "target" insertion, then use this "template +2aa" model as template for building the model of the target???? 2. The residues flanking the insertions also belong to the loop regions (of the template), so, my question is, when we do loop modelling, do we need to model the whole piece of loop for accuracy?? 3. When we generate loop models, do you model one loop and then the other? Since I have two loop regions, I wonder if I should build (~500) models for one regions and then another set for the other region? Does one loop region actually affect the conformation of the other loop? Do you think it's necessary to build them both at the same time? Thank you very much for answering the questions. Have a great day. Sincerely, Jasmine --------------------------------- Do you Yahoo!? Next-gen email? Have it all with the all-new Yahoo! Mail Beta.

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alignment using multiple templates
by Mike White 15 Jun '06

15 Jun '06

HI there, I am working my way through the tutorials, playing with the Python scripts to get a better understanding of how things work. I have successfully done a multiple structural alignment using a modified version of the salign.py script in the advanced tutorial aligning multiple sequences for a protein from several different species using the pdb files as input. The protein is a homopentamer, and using the example script, I aligned the "A" chains and everything worked fine. Since I really want to work on modeling a homopentamer, I then tried to do the alignment on the pentamers. I receive the following error: ************************************************************************* linux:/home/mike/Modeller_files/Modelling_projects/Test_run/Mult_align # mod8v2 salignPentamer.py Traceback (most recent call last): File "salignPentamer.py", line 11, in ? mdl = model(env, file=code, model_segment=('FIRST:@, LAST:')) File "/usr/bin/modeller8v2/modlib/modeller/model.py", line 23, in __init__ self.read(io, aln, libs, **vars) File "/usr/bin/modeller8v2/modlib/modeller/model.py", line 40, in read io=io.modpt, libs=libs.modpt, **vars) File "/usr/bin/modeller8v2/modlib/modeller/util/top.py", line 189, in read_model return _modeller.read_model(mdl, aln, io, libs, *args) ValueError: Expected a sequence for model_segment ************************************************************************* I assume that the problem is in reading the pdb files and getting the information.The pdb files do contain the chain ID's (A-E). Here is the Python script I used, which is essentially a slightly modified version of the example script: ********************************************************************* from modeller import * log.verbose() env = environ() env.io.atom_files_directory = './:../atom_files/' aln = alignment(env) for (code, chain) in (('1i9b', 'A'), ('2br7', 'A'), ('2bj0', 'A')): mdl = model(env, file=code, model_segment=('FIRST:@, LAST:')) aln.append_model(mdl, atom_files=code, align_codes=code+chain) for (weights, write_fit, whole) in (((1., 0., 0., 0., 1., 0.), False, True), ((1., 0.5, 1., 1., 1., 0.), False, True), ((1., 1., 1., 1., 1., 0.), True, False)): aln.salign(rms_cutoffs=(3.5, 6., 60, 60, 15, 60, 60, 60, 60, 60, 60), normalize_pp_scores=False, rr_file='$(LIB)/as1.sim.mat', overhang=30, gap_penalties_1d=(-450, -50), gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0, dendrogram_file='fm00495.tree', alignment_type='tree', # If 'progresive', the tree is not # computed and all structues will be # aligned sequentially to the first feature_weights=weights, # For a multiple sequence alignment only # the first feature needs to be non-zero improve_alignment=True, fit=True, write_fit=write_fit, write_whole_pdb=whole, output='ALIGNMENT QUALITY') aln.write(file='achbpsPentamer.pap', alignment_format='PAP') aln.write(file='achbpsPentamer.ali', alignment_format='PIR') aln.salign(rms_cutoffs=(1.0, 6., 60, 60, 15, 60, 60, 60, 60, 60, 60), normalize_pp_scores=False, rr_file='$(LIB)/as1.sim.mat', overhang=30, gap_penalties_1d=(-450, -50), gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0, dendrogram_file='1is3A.tree', alignment_type='progressive', feature_weights=[0]*6, improve_alignment=False, fit=False, write_fit=True, write_whole_pdb=False, output='QUALITY') ********************************************************************************** the only change that I made from the script that worked on the single subunits was to change the "model_segment" parameters from "('FIRST:'+chain, 'LAST:'+chain)" to "('FIRST:@, LAST:'))". I couldn't find anything in the Online manual concerning the arguments on the line before (for (code,chain) in.....)- should I have replaced chain "A" with something else to read the entire set of chains? Thanks for whatever help you can provide. I am sure that as I get deeper into things that I'll have more questions- hopefully not so basic. Mike White

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Modeling a Chimera
by Toty Santos 14 Jun '06

14 Jun '06

Hi dears, I am a starting model buiter and i´d like to know how i can make a model like this : I have a bifuncional enzime with two domains. But in the PDB i have as a model different structures : One for domain A and other to domain B. And i´d like to build a model with this two domains together. It is not a dimer, it a single enzime with two diferente domains. And i´d like to know tto, what i will do with the linker resudues between this both domains !! I anybody can help me, please be detalist cause i am a start user i am using Modeller 8v0 thanks a Lot Marcos Tadeu dos Santos Undergratuated Student UNICAMP - BRAZIL _________________________________________________________________ COPA 2006: (¯`·._.·[ Ooooooola ]·._.·´¯) e + frases para seu MSN Clique aqui! http://copa.br.msn.com/extra/frases/

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rdpir___648E> Alignment sequence not found in PDB file
by Michael Mazanetz 14 Jun '06

14 Jun '06

Dear MODELLER users, I get this error message " rdpir___648E> Alignment sequence not found in PDB file: 1 ../atom_files\1ba4.pdb " in my log file when I try and run a homology model. When I reduce the number of residues in the sequence to just four the model runs OK. What is wrong, can anyone suggest anything?? I've enclosed my files :screen output, B04_2742_111_002.ali, Loop-005.py and Loop-005.log And the -v command always gives an error too?? regards and thanks in advance. Mike The screen output is: C:\Program Files\Modeller8v2\examples\automodel>mod8v2 loop-005.py -v 'import site' failed; use -v for traceback Traceback (most recent call last): File "loop-005.py", line 24, in ? a.make() # do the actual homology modelling File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\loopmodel.py", line 28, in make automodel.make(self, exit_stage) File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 100, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 318, in homcsr aln = self.read_alignment() File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 312, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "C:\Program Files\Modeller8v2\modlib\modeller\alignment.py", line 36, in append return self.__int_append('alignment.append', io, libs, vars) File "C:\Program Files\Modeller8v2\modlib\modeller\alignment.py", line 68, in__int_append libs=libs.modpt, **vars) File "C:\Program Files\Modeller8v2\modlib\modeller\util\top.py", line 33, in read_alignment return _modeller.read_alignment(aln, io, libs, *args) _modeller.error: rdpir___648E> Alignment sequence not found in PDB file:1 ../atom_files\1ba4.pdb B04_2742_111_002.ali file >P1;1ba4 structureX:1ba4:.:.:.:.: MENFQKVEKI GEGTYGVVYK ARNKLTGEVV ALKKIRXDTE TEGVPSTAIR EISLLKELNH PNIVKLLDVI HTENKLYLVF EFLHQDLKKF MDAS------* >P1;1M8Qb structureX:1M8Qb:.:.:.:.: ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ----KQPRQY* >P1;1bb2 sequence:1ba2:.:.:.:. MEDYTKIEKI GEGTYGVVYK GRHKTTGQVV AMKKIRLESE EEGVPSTAIR EISLLKELRH PNIVSLQDVL MQDSRLYLIF EFLSMDLKKY LD-SIPPGQY* Loop-005.py file # Homology modelling by the automodel class from modeller.automodel import * # Load the automodel class 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' a = loopmodel(env, alnfile = 'B04_2742_111_002.ali', # alignment filename knowns = ('1ba4','1M8Qb'), # codes of the templates sequence = '1ba2') # 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 = 1 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() # do the actual homology modelling Loop-005.log file rdpir___648E> Alignment sequence not found in PDB file: 1 ../atom_files\1ba4.pdb This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Modeling a Chimera
by Toty Santos 14 Jun '06

14 Jun '06

Hi dears, I am a starting model buiter and i´d like to know how i can make a model like this : I have a bifuncional enzime with two domains. But in the PDB i have as a model different structures : One for domain A and other to domain B. And i´d like to build a model with this two domains together. It is not a dimer, it a single enzime with two diferente domains. And i´d like to know tto, what i will do with the linker resudues between this both domains !! I anybody can help me, please be detalist cause i am a start user i am using Modeller 8v0 thanks a Lot Marcos Tadeu dos Santos Undergratuated Student UNICAMP - BRAZIL _________________________________________________________________ Você sabe em qual Copa o Pelé vestiu a camisa 10 pela 1a. vez? http://copa.br.msn.com/extra/curiosidades/1958/

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Imposing dihedral restraints
by Vivek Sharma 14 Jun '06

14 Jun '06

Dear Benn, I am having some troubles in putting dihedral restraints in the system I am modelling. Firstly, I should say I want to put backbone angles (phi/psi) into a stretch of 5 amino acid residues. I mention the values (these values are from database, in fact are right and do exist in one protein) with the std. deviation value ~ 15deg. And, I am using Modeller 7v7, sorry I am slow in updating myself ;). So for e.g. I put a dihedral restraint (say phi for e.g.) for a residue like this: SET ATOM_IDS = 'C:317' 'N:318' 'CA:318' 'C:318' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 3 11 4 2 0 -1 0.261 So now you can see here; Form is 3 Modality is 1 Feature is 3 (dihedral angle) group is 11 (Mainchain phi dihedral restraints) Numb_atoms = 4 Numb_parameters = 2 0 Value of angle in radians Std. deviation in radians. Now when I run modeller with such restraints, in the finally obtained models, I dont see these exact values of restraints, which we mentioned explicitly, taken in by the model. Why this is so? The values of these mentioned dihedral restraints in the modelled models are far from the prescribed values. Secondly, though I dont see any violation also in concern to these values, i.e. if I have understood correctly, then violation will be reported in the log file if (optimized value - value mentioned by used)/(std. deviation) > 4.5 (approximately something like that). So this makes clear that why violation is not reported, because our values (diff/std. devn) are less than 4.5. But the question is, that when I give value of 15 degree as std. deviation (which I have to, I will come to this point later!) , then difference between optimsed value and mentioned value ~ 60 degrees, and that is very much. So again what I say is that I want to put certain values of dihedrals (backbone angles in fact) in the model, but values obtained for these angles in optimised models are far from the values mentioned in by me (because range of difference is ~60 degrees), though there are no violations reported, probably because of the above mentioned reason. PLease tell me what to do in this concern. Now as I said above that I am giving 15deg as std. deviation,but when I use smaller values like 5deg or so, the program is getting failed, it seems that it is getting difficult for it to optimise the system, with smaller values of std. deviation. Also, please tell me how to solve this problem. Last but not least, what I tried or trying is that creating the gaps in this section of 5 residues, where I am imposing backbone dihedrals, so that MODELLER doesnt find any equivalent residues in that position in templates and probably reduces the number of restraints, and in that case I may be able to impose my restraints well enough for these five residues, but still results doesnt seems to go hand in hand. Any comments in this concern also will be helpful. Details: there are two templates, MD_LEVEL is refine_3, our own alignment and paramters are used. So overall these are the problems I am at the moment facing, so any comments/details, will be very helpful. PS: The subject is different from 'Problem', :). Thanks in advance, br, Vivek Sharma University of Helsinki.

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Modeling core residues without loop regions
by Vimalkumar Velayudhan 13 Jun '06

13 Jun '06

Dear MODELLER users, I was looking for answers to the following questions? 1. What is the best approach to model proteins with large insertions (approximately 50residues) at different parts of the protein. Example AAAAAA---------------------------------BBBBBB---------------------------------------------CCCC Even if the alignment is good, I get an exceeded maxmolpdf error in the model building stage. I am not sure what value to set for the maxmolpdf . 2.Is it possible to build only the core residues without the insertions? It would be helpful if you can point me to references related to the same. -- Vimalkumar Velayudhan

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Re: [modeller_usage] How can I get MolPDF of an existed PDB file of an model
by Modeller Caretaker 09 Jun '06

09 Jun '06

Yun He wrote: > On Thursday 08 June 2006 09:40, you wrote: >> The PDB files produced by Modeller also contain the molpdf, as a REMARK >> at the top of the file, so you can just read this. If you refine the >> structure, you should write out a new PDB file, which will contain the > ~~~~~~~~~~~~~ write out?? If I refine this model with > Refmac5 in CCP4, the refined model written by Refmac5 doesn't contain any > header remark about molpdf, how should I get the molpdf? Is this molpdf the > same as the one of the model not refined, or there are any ways to > re-calculate its molpdf? Scoring functions used by different programs are almost never comparable, so you can't do this. All you can do is to, like I said, write out the refined structure and then recalculate its molpdf in Modeller. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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loop modelling
by hori koshii 08 Jun '06

08 Jun '06

Does MODELLER has a limitation for loop modelling up to 12 or 14 residues? What if I have 20 residues? Could you please give me some suggestions how to model a loop like this please? Thanks in advance! :) __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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DOPE profile
by Tom Burghardt 07 Jun '06

07 Jun '06

Modellers I would like to make a DOPE profile for a modeled protein containing a chemically modified side chain. I used the script suggested in the Advanced Tutorial with the following lines to read the library files containing information about the modified residue. env = environ(restyp_lib_file='${LIB}/restyp_tom.lib') env.libs.topology.read(file='$(LIB)/top_heav_tom.lib') # read topology env.libs.parameters.read(file='$(LIB)/par_tom.lib') # read parameters The DOPE profile is created by the script but the modified residue is left out of the profile. Any suggestions would be appreciated. Tom -- Tom Burghardt Department of Physiology and Biomedical Engineering Mayo Clinic

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