January 2011 - modeller_usage

Loop modeling
by bharat lal 01 Mar '11

01 Mar '11

Hi, I have modelled a protein using secondary structure restrained script... The model seems to be perfectly fine .. but one portion of the model is converted into a helix which has to be a loop according to the template .. how can I force that region to be a loop ??? ------------ Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 E-mail : monu46010(a)yahoo.com

3 3

Differences using Xeon vs Opteron systems
by Robert Healey 15 Feb '11

15 Feb '11

Hello. I'm the systems administrator for a research lab using Modeller 9v3. I've installed the x86_64 RPM file on a pair of Xeon X5355 based systems and some Opteron 6136 based systems. The researchers are reporting getting radically different results between these two systems. I've done some testing and Opteron 252 based systems give the same results as the Opteron 6136 systems and Xeon X5570 systems give the same results as the Xeon X5355. I'm working on getting a set of results I can post, but has anyone seen anything like this before? I was being shown summaries where the final results were different in value by 1.5 Thank you. -- Bob Healey Systems Administrator Biocomputation and Bioinformatics Constellation and Molecularium healer(a)rpi.edu (518) 276-4407

2 3

loop error
by albert 31 Jan '11

31 Jan '11

Dear: I am trying to refine my model with loop refine protocol. But it is always said: ------------------------------------------------------------------------------------------------------- File "/usr/lib64/python2.4/site-packages/modeller/coordinates.py", line 226, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib64/python2.4/site-packages/modeller/util/modutil.py", line 19, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib64/python2.4/site-packages/modeller/coordinates.py", line 289, in _indxres raise KeyError("No such residue: %s" % indx) Here is my script, could you please give me some advices? ---------------------------------------------------------------------------------------- # Loop refinement of an existing model from modeller import * from modeller.automodel import * log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms (necessary) class MyLoop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # One loop from residue 19 to 28 inclusive return selection(self.residue_range('273', '283')) #return selection(self.residue_range('1:', '4:')) m = MyLoop(env, inimodel='input.pdb', # initial model of the target sequence='model') # code of the target m.loop.starting_model= 0 # index of the first loop model m.loop.ending_model = 100 # index of the last loop model m.loop.md_level = refine.very_fast # loop refinement method m.make() KeyError: 'No such residue: 206:'

2 1

Fw:loop error
by albert 29 Jan '11

29 Jan '11

Dear: I am trying to refine my model with loop refine protocol. But it is always said: ------------------------------------------------------------------------------------------------------- File "/usr/lib64/python2.4/site-packages/modeller/coordinates.py", line 226, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib64/python2.4/site-packages/modeller/util/modutil.py", line 19, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib64/python2.4/site-packages/modeller/coordinates.py", line 289, in _indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 273:' Here is my script, could you please give me some advices? ---------------------------------------------------------------------------------------- # Loop refinement of an existing model from modeller import * from modeller.automodel import * log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms (necessary) class MyLoop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # One loop from residue 19 to 28 inclusive return selection(self.residue_range('273', '283')) #return selection(self.residue_range('1:', '4:')) m = MyLoop(env, inimodel='input.pdb', # initial model of the target sequence='model') # code of the target m.loop.starting_model= 0 # index of the first loop model m.loop.ending_model = 100 # index of the last loop model m.loop.md_level = refine.very_fast # loop refinement method m.make() KeyError: 'No such residue: 206:'

1 0

mercury ions ignored by model.write_data()
by Yingjie Lin 26 Jan '11

26 Jan '11

Hi All, I found that model.write_data() ignores mercury ions (HG) when writing .ngh files (e.g. 1AVN.pdb, 1OKM.pdb). It also ignores UNX (UNKNOWN ATOM OR ION), in which case I understand. I checked whether mercury ions are ignored because it's not in modeller-9v8/modlib/restyp.lib, but I don't think so because LI1 (in 2I21.pdb) and DOD (in 1CQ2.pdb) are not ignored. Is there a reason why mercury ions should be ignored? Are there any other specific records that model.write_data() will ignore? Thank you! - Yingjie

2 1

loop modeling parallel-queue
by David Rodríguez 26 Jan '11

26 Jan '11

Hi, Let's suppose we are sending a protein to refine four of its loops, eight repeats (32 loops). If I spawn eight Slaves (job().append()), a single model is sent to each slave and each slave compute the four loops. Now suppose we are sending the same protein, to refine four of its loops just one time (4 loop). Spawning the same eight Slaves, the model is sent to just one Slave, and that slave compute all of the four loops alone (i.e. modeller is not parallelizing). My question is: is there any difference between a) sending the eight jobs from within the modeller script or b) sending one job after another to a third queue software initializing the enviroment with env = environ(0 - random.randrange(2, 50000)) #A different random seed each time. or is modeller taking into account previous results? Thanks in advance, -- David Rodríguez Díaz, PhD Student Fundación Pública Galega de Medicina Xenómica (SERGAS) Santiago de Compostela (Spain) http://webspersoais.usc.es/persoais/david.rodriguez.diaz <http://webspersoais.usc.es/persoais/david.rodriguez.diaz>

3 4

Loop modeling while restraining the secondary structure
by bharat lal 25 Jan '11

25 Jan '11

Hi, Thanks for the help regrading model-loop-define.py script. I have one doubt in model selection .. The number of residues that has to be mentioned for restraining should according to the target sequence only know ?? .. Also, I generated some 5 models while restraining some portion of the sequence as beta strands and after seeing all the structures I found that its model 3 that is having perfectly restrained beta sheets as compared to others but its DOPE score is more as compared to other structures . In this type of situation how do we have to select the correct model ?? Here's the list of energies that I got : >> Summary of successfully produced models:Filename molpdf DOPE score GA341 score----------------------------------------------------------------------target.B99990001.pdb 1552.05176 -25341.12891 1.00000target.B99990002.pdb 1485.22974 -25387.23438 1.00000target.B99990003.pdb 1559.28723 -25382.83984 1.00000 (perfectly restrained str.)target.B99990004.pdb 1483.82568 -25213.86523 1.00000target.B99990005.pdb 1402.83508 -25525.49023 1.00000 Also, I would like to ask one more thing about restraining structure that while giving the residue range generally last 2 or some times 1 residue/s doesnot retain the restrained structure .. In that case what do i need to do ?? After doing the restrained modeling is it required to do loop refinement .. as I am doing loop refinement also by generating some 50 structures and then finally selecting the one with low DOPE score .. Is this strategy right or wrong ?? -------------- Bharat

2 1

how satisfactory relative orientation of modeled domains can be achieved in two matches cases
by Maria Persico 25 Jan '11

25 Jan '11

Hello, I am exploring ModBase to build a model for the REcQ2 of arabidopsis Thaliana(swiss prot acc: Q9FT73). ModBase found 2 structures matching this target and after downloading the coordinates file and also the showfile.chimerax file, I was able to visualize with chimera both structures with apparently a satisfactory relative orientation. Below I copy-paste the target coverage: 2v1xA (63-592) crystal structure of human recq-like dna helicase 1wudA (531-602) e. coli recq hrdc domain I wanted to know if there is an optimization step in the ModBase pipeline to achieve this and if it is referenced somewhere....and if not, which modules-scripts are available? Thanks for your attention, Maria Persico Quoting modeller_usage-request(a)salilab.org: > Send modeller_usage mailing list submissions to > modeller_usage(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. Re: restraining secondary structure (Modeller Caretaker) > 2. Re: BLK usage => mainy chains (Modeller Caretaker) > 3. Re: Loop Modeling (Modeller Caretaker) > 4. Loop modeling while restraining the secondary structure > (bharat lal) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 24 Jan 2011 14:49:01 -0800 > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: [modeller_usage] restraining secondary structure > To: bharat lal <monu46010(a)yahoo.com> > Cc: modeller <modeller_usage(a)salilab.org> > Message-ID: <4D3E01DD.9030008(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 1/24/11 1:00 AM, bharat lal wrote: >> I am using the following script for restraining the beta strands in my >> protein (after searching the mailing archives):- > > Your script will not work because you are using the automodel class > rather than your custom 'mymodel' class. Replace > a = automodel(env, > with > a = mymodel(env, > > This also looks like a very old Modeller script (perhaps for Modeller > 8). The way secondary structure restraints are defined has changed. See > http://salilab.org/modeller/9v8/manual/node27.html > for the correct syntax for adding a secondary structure restraint. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 2 > Date: Mon, 24 Jan 2011 14:51:01 -0800 > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: [modeller_usage] BLK usage => mainy chains > To: Isaure Chauvot de Beauchene <ichauvot(a)lbpa.ens-cachan.fr> > Cc: modeller_usage(a)salilab.org > Message-ID: <4D3E0255.1050307(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 1/24/11 6:56 AM, Isaure Chauvot de Beauchene wrote: >> I try to build a modele with 2 protein templates. I want to modelise >> just one loop of 1pkg, part of it on the template 3A2M, the rest of the >> loop de novo. The rest of 1pkg must not be changed, so I put it as BLK: > > BLK residues are really designed for modeling ligands and other things > that are not proteins. If you only want Modeller to optimize part of > your protein, see > http://salilab.org/modeller/9v8/manual/node23.html > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 3 > Date: Mon, 24 Jan 2011 14:56:19 -0800 > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: [modeller_usage] Loop Modeling > To: bharat lal <monu46010(a)yahoo.com> > Cc: modeller <modeller_usage(a)salilab.org> > Message-ID: <4D3E0393.2020703(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 1/24/11 12:01 AM, bharat lal wrote: >> I want to graft the loop from some other protein taken from pdb to my >> protein structure. > > You could use multiple-template modeling to achieve this. Alternatively, > you could manually combine the two PDB files, using a PDB viewer or even > by editing the files in a text editor. > >> I tried modeling it on my own but some parts of the >> secondary structure (beta sheet) also change into loop while loop >> modeling .. > > That is hardly surprising - loop modeling does not use any information > from the template. > >> So I want to fix those two ends of the beta sheet where the >> loop is present so that these end should not change to loop region. > > If you don't want to subject the beta sheet to loop modeling, simply > don't select those residues in the select_loop_atoms function: > http://salilab.org/modeller/9v8/manual/node34.html > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 4 > Date: Tue, 25 Jan 2011 11:18:50 +0530 (IST) > From: bharat lal <monu46010(a)yahoo.com> > Subject: [modeller_usage] Loop modeling while restraining the > secondary structure > To: modeller <modeller_usage(a)salilab.org> > Message-ID: <274112.20221.qm(a)web94710.mail.in2.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > Thanks for the help regrading model-loop-define.py script. I have > one doubt in model selection .. The number of residues that has to > be mentioned for restraining should according to the target sequence > only know ?? .. > Also, I generated some 5 models while restraining some portion of > the sequence as beta strands ?and after seeing all the structures I > found that its model 3 that is having perfectly restrained beta > sheets as compared to others but its DOPE score is ?more as compared > to other structures . In this type of situation how do we have to > select the correct model ?? Here's the list of energies that I got : >>> Summary of successfully produced models:Filename ? ? ? ? ? ? ? ? ? >>> ? ? ? ?molpdf ? ? DOPE score ? ?GA341 >>> score----------------------------------------------------------------------target.B99990001.pdb ? ? ? ? ?1552.05176 ? -25341.12891 ? ? ? ?1.00000target.B99990002.pdb ? ? ? ? ?1485.22974 ? -25387.23438 ? ? ? ?1.00000target.B99990003.pdb ? ? ? ? ?1559.28723 ? -25382.83984 ? ? ? ?1.00000 (perfectly restrained str.)target.B99990004.pdb ? ? ? ? ?1483.82568 ? -25213.86523 ? ? ? ?1.00000target.B99990005.pdb ? ? ? ? ?1402.83508 ? -25525.49023 ? ? ? >>> ?1.00000 > > Also, I would like to ask one more thing about restraining structure > that while giving the residue range generally last 2 or some times > 1 residue/s doesnot retain the restrained structure .. In that case > what do i need to do ?? > After doing the restrained modeling is it required to do loop > refinement .. as I am doing loop refinement also by generating some > 50 structures and then finally selecting the one with low DOPE score > .. Is this strategy right or wrong ??? > > > -------------- > Bharat > > > >

2 1

Problem applying helix restraints to a homodimer model ..
by Sergio Garay 25 Jan '11

25 Jan '11

Dear Modeller's users I want to add a helix restraint to some residues in each monomer of my homodimer model, I followed the example given in Modeller 9v8 Manual but It gives me the following error (Is it a residue numbering problem?): KeyError: 'No such residue: 29:' This is my alignment file, which worked well without adding the helix restraint: >P1; TCP15_dimer2 sequence:TCP15_dimer2:::::::0.00:0.00 -KDRHTKVEGRGRRIRMPAMCAARVFQLTRELGHKSDGE-----------TIEWLLQQAE P-AVIAA----- / -KDRHTKVEGRGRRIRMPAMCAARVFQLTRELGHKSDGE-----------TIEWLLQQAE P-AVIAA----- / .................. / .................. * >P1; 1nlw_D_E structureX:1nlw_D_E:503:D:819:J:::-1.00:-1.00 -RSTHNEMEKN-RRAHLRLSLE-KLKGL-----------VPLGPDSSRHTTL-SLLTKAK LHIKKLE----- / --AHHNALERK-RRDHIKDSFH-SLRDS-----------VPSLQ-GEKASRA-QILDKAT EYIQYMRR---- / .................. <--- DNA chain 1 / .................. <---DNA chain 2 * This is the script I used: from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Read in HETATM records from template PDBs env.io.hetatm = True <---- This is added because my model also include a small DNA molecule class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Residues restraints for the first monomer: rsr.add(secondary_structure.alpha(self.residue_range('29:', '32:'))) rsr.add(secondary_structure.alpha(self.residue_range('38:', '39:'))) # Residues restraints for the second monomer: rsr.add(secondary_structure.alpha(self.residue_range('111:', '114:'))) rsr.add(secondary_structure.alpha(self.residue_range('121:', '122:'))) a = MyModel(env, alnfile = 'alignment_2.ali' , # alignment filename knowns = '1nlw_D_E' , # codes of the templates sequence = 'TCP15_dimer2') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 5 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling Any suggestion will be appreciated -- Sergio Garay Dr. en Ciencias Biológicas Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

2 1

Loop Modeling
by bharat lal 24 Jan '11

24 Jan '11

Hi, I want to graft the loop from some other protein taken from pdb to my protein structure. I tried modeling it on my own but some parts of the secondary structure (beta sheet) also change into loop while loop modeling .. So I want to fix those two ends of the beta sheet where the loop is present so that these end should not change to loop region. Is it possible using modeller and if it's possible .. is it logically correct as during my modeling study I found that some part of beta sheets get converted to loop .. so fixing the ends of beta sheet while loop modeling would be sensible or not ?? Pls guide ----------------- Bharat

2 1