August 2010 - modeller_usage

R: modelling discarding part of a template
by Thomas Evangelidis 01 Sep '10

01 Sep '10

> You have to either keep the complete template sequence in the PDB file, > or modify the template PDB to remove the residues you don't want. An > alignment that achieves what you want without modifying the PDB is: > > target: AAAAAAAAAAA-------AAAAAA > template 1: BBBB-------BBBBBBBBBBBBB > template 2: ZZZZZZZZZZZ-------ZZZZZZ > > Ben Webb, Modeller Caretaker > > Is it algorithmically difficult to add a function that will select a range of residue in one template and Modeller will exclude them without touching the alignment? When having multiple templates and several unwanted regions this procedure becomes very tedious.

2 2

unable to read structural information
by meier＠lmb.uni-muenchen.de 31 Aug '10

31 Aug '10

Hi all, suppose I have the following simple "dummy" py-modeller script: from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = '<path to pdb>' # containing d1f0la3.pdb a = automodel(env, alnfile = '<my_pir_file.pir>', # alignment filename knowns = 'd1f0la3', # codes of the templates sequence ='d1f0la3') # code of the target a.starting_model = 1 a.ending_model = 3 a.make() and the corresponding pir file: >P1;d1f0la3 sequence:d1f0la3: 1: : 180: :f.1.2.1 (A;201-380) Diphtheria toxin, middle domain {Corynebacterium diphtheriae [TaxId; 1717]} PDB; d1ddta3 d1p3gb_ d1p3gf_ d1p3pb_ d1p3pf_ d1p3bf_ d1p3ib_: : 0.00: 0.00 CINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKT TAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVESIINLFQVVHNSYNRPAY* >P1;d1f0la3 structureX:d1f0la3: :A: :A:f.1.2.1 (A201-380) Diphtheria toxin, middle domain {Corynebacterium diphtheriae [TaxId 1717]} PDB d1ddta3 d1p3gb_ d1p3gf_ d1p3pb_ d1p3pf_ d1p3bf_ d1p3ib_:Corynebacterium diphtheriae [TaxId; 1717]:-1.00:-1.00 CINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKT TAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGEL--IGFAAYNFVESIINLFQVVHNSYNRPAY* Then I get the following error when executing the script: Traceback (most recent call last): File "/cluster/tmp/armin/test/d1f0la3_d1f0la3_1.py", line 14, in <module> a.make() File "/cluster/bioprogs/modeller9v5_RSR/modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/cluster/bioprogs/modeller9v5_RSR/modlib/modeller/automodel/automodel.py", line 425, in homcsr self.check_alignment(aln) File "/cluster/bioprogs/modeller9v5_RSR/modlib/modeller/automodel/automodel.py", line 407, in check_alignment aln.check() File "/cluster/bioprogs/modeller9v5_RSR/modlib/modeller/alignment.py", line 191, in check self.check_structure_structure(io=io) File "/cluster/bioprogs/modeller9v5_RSR/modlib/modeller/alignment.py", line 200, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.ModellerError: check_a_282E> Unable to read structural information for alignment sequence: 1 d1f0la3 This command requires structures. Any ideas whats wrong? Thanks in advance Armin

2 1

modeller usage under Cyg Win
by Andrew Voronkov 26 Aug '10

26 Aug '10

What version of Modeller is better to use under Cyg win on 64 bit Windows system? I have problems while using the Windows version of the program. Sincerely yours, Andrew

2 1

modeling mutant proteins
by Peter K 26 Aug '10

26 Aug '10

Hi, i would like to know the tool which uses modeller for prediction of structure of mutants and analyze its stability and change in activity in mutant proteins.Can any one suggest a tool for it.

2 1

initial model
by sdh 17 Aug '10

17 Aug '10

Hello All, I want to model a multi-domain protein. Thus, I aligned manually all templates (corresponding to the individual domains) and used them as an input for Modeller. (Note that the templates overlap only over few residues.) However, when I compared the initial model (.ini) to the aligned templates, I saw that Modeller did something more than just transferring the coordinates from the templates. Namely, the relative orientation of domains is not as in my structural alignment. Is thee any way to force Modeller to use exactly the input coordinates? initial_malign3d is set to False and default transfer_xyz() is used Thanks for help! Staszek

2 1

very_fast()
by sdh 17 Aug '10

17 Aug '10

Hello, Does usage of "very_fast()" deactivates restraints defined by "nonstd_restraints()"? sdh

2 1