- modeller_usage - salilab.org

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

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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

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BLK usage => mainy chains
by Isaure Chauvot de Beauchene 24 Jan '11

24 Jan '11

Hello, 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: P1;1pkg structureX:1pkg:1:A:280:A:::: .............................................................................. ........................................-------------------------------------- -------------------------------------------................................... .............................................................................. .................................................* P1;3A2M structureX:3A2M:283:A:305:A:::: ------------------------------------------------------------------------------ ----------------------------------------QEDHADAIGRSVAGWIAGIEAVR--------------- ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ -------------------------------------------------* P1;KID sequence:KID:1:A:361:A:::: .............................................................................. ........................................KRDSFICSKQEDHAEAALYKNLLHSKESSCSDSTNEYM DMKPGVSYVVPTKADKRRSVRIGSYIERDVTPAIMEDDELALD................................... .............................................................................. .................................................* I get a model with 3 chains instead of one. How can I get a one-chain model? All atoms in the pdb files are like "ATOM". Should I change it in "HETATM"? Thanks a lot in advance, Isaure -- Isaure Chauvot_de_Beauchêne ichauvot(a)lbpa.ens-cachan.fr PhD Student Laboratoire de Biolgie et Pharmacologie Appliquée (Dir J.-F. Mouscadet) CNRS - Ecole Normale Supérieure de Cachan Equipe BioInformatique, Modélisation et Dynamique Moléculaire (BIMoDyM) (Dir Luba.Tchertanov) 61 Av du Président Wilson 94230 Cachan France

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restraining secondary structure
by bharat lal 24 Jan '11

24 Jan '11

Hi, I am using the following script for restraining the beta strands in my protein (after searching the mailing archives):- # comparative modeling from modeller.automodel import * # Load the automodel class class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints rsr.make(aln, restraint_type='STRAND',residue_ids=('171','172'))log.very_verbose() # request verbose outputenv = environ() # create a new MODELLER environment to build this model in# directories for input atom filesenv.io.atom_files_directory = ['.', '../atom_files'] a = automodel(env, alnfile = 'alignment.ali', # alignment filename knowns = ('template','template2'), # codes of the templates sequence = 'target') # code of the targeta.starting_model= 1 # index of the first modela.ending_model = 5 # index of the last model# (determines how many models to calculate)a.make() # do the actual homology modelling ------------------------------I have a doubt regarding this script as didn't get the desired restraints in the modelled protein.The residue_ids that we have to provide should be a range as my loop regions exists between two ends of beta strands i.e. 171 and 175 amino acid . 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

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model_addrsr.py
by Koushik A C 24 Jan '11

24 Jan '11

Hi , I am not able to model beta sheets even if i am using model_addrsr,py file. Can anyone please help me out..!! This is the script file i used. # Addition of restraints to the default ones 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'] class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Add some restraints from a file: # rsr.append(file='my_rsrs1.rsr') # Residues 20 through 30 should be an alpha helix: # rsr.add(secondary_structure.alpha(self.residue_range('269:', '302:'))) # rsr.add(secondary_structure.alpha(self.residue_range('171:', '189:'))) # rsr.add(secondary_structure.alpha(self.residue_range('171:', '189:'))) # rsr.add(secondary_structure.alpha(self.residue_range('171:', '189:'))) # rsr.add(secondary_structure.alpha(self.residue_range('209:', '228:'))) # rsr.add(secondary_structure.alpha(self.residue_range('236:', '255:'))) # rsr.add(secondary_structure.alpha(self.residue_range('335:', '353:'))) # Two beta-strands: # rsr.add(secondary_structure.strand(self.residue_range('148:', '154:'))) rsr.add(secondary_structure.strand(self.residue_range('65:', '75:'))) # An anti-parallel sheet composed of the two strands: # rsr.add(secondary_structure.sheet(at['N:1'], at['O:14'], # sheet_h_bonds=-5)) # Use the following instead for a *parallel* sheet: # rsr.add(secondary_structure.sheet(at['N:1'], at['O:9'], # sheet_h_bonds=5)) # Restrain the specified CA-CA distance to 10 angstroms (st. dev.=0.1) # Use a harmonic potential and X-Y distance group. # rsr.add(forms.gaussian(group=physical.xy_distance, # feature=features.distance(at['CA:35'], # at['CA:40']), # mean=10.0, stdev=0.1)) a = MyModel(env, alnfile = 'target-temp.ali', # alignment filename knowns = 'template', # codes of the templates sequence = 'target') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 2 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs)

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Problem for a protein model
by Bishwajit Das 24 Jan '11

24 Jan '11

I am doing a protein model name RFX5 in a modeller in windows operating system,but i can't understand which command i use and how i search a template and doing model.Please tell me the command name and example also. -- * BISHWAJIT DAS* *+91-9433237920* KOLKATA

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 9
by Ashish Runthala 24 Jan '11

24 Jan '11

Respected Sir, I tried your approach. It works. But still it wasn't working out the way i want it. Is it possible that you can find the "final max quality" for a model decoy with its native state experimental structure. salign_iterative does work properly for 2 crystal structures but how to make it work for both template/Native State & Model structure. Thanks, Ashish ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Saturday, January 22, 2011 2:59:16 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 9 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. Regarding Salign (Ashish Runthala) 2. model_addrsr.py (Koushik A C) 3. Re: model_addrsr.py (Modeller Caretaker) 4. Re: Regarding Salign (Modeller Caretaker) ---------------------------------------------------------------------- Message: 1 Date: Fri, 21 Jan 2011 08:41:47 +0530 (IST) From: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Subject: [modeller_usage] Regarding Salign To: modeller <modeller_usage(a)salilab.org> Message-ID: <32062261.262361295579507848.JavaMail.root(a)mailserver.bits-pilani.ac.in> Content-Type: text/plain; charset=utf-8 I checked salign too. It considers penalties on primary sequence and then moves to the structural alignment of considered structures before adding target sequence according to generated structural topology. But will you pass me the script lines which aligns structures at 1,2,3,4Angstroms. My another doubt is that how the considered structures are considered all together for each of these distance cutoffs. Is this like nC2 combination based structural alignment satisfaction of restraint matrix generated. Show me where these 1,2,3,4 Angstroms are available in salign_iterative. I couldn't find them. Thanks, Ashish ------------------------------ Message: 2 Date: Fri, 21 Jan 2011 13:23:40 +0530 (IST) From: Koushik A C <011113027(a)sastra.edu> Subject: [modeller_usage] model_addrsr.py To: modeller_usage(a)salilab.org Message-ID: <992863059.70038.1295596420282.JavaMail.root(a)mail.sastra.edu> Content-Type: text/plain; charset="utf-8" Hi, I am not able to model beta sheets even if i am using model_addrsr,py file. Can anyone please help me out..!!

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Problem modelling protein dimer close to DNA ...
by Sergio Garay 24 Jan '11

24 Jan '11

Dear Modeller's Users: I'm trying to model a protein dimer interacting with a small DNA molecule. Following the manual instructions I was able to build my dimer using: >P1; my_target xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx --> first monomer / yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy --> second monomer * >P1; my_template hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh --> first monomer / kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk ---> second monomer * But I have some problems to add my DNA molecule as an additional restraint: I added to my script: env.io.hetatm = True And I also added my DNA molecule (all the DNA atoms were named HETATM) into the template pdb and modified my alignment in this way: >P1; my_target xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx --> first monomer ---------- --> alignment of extra dna residues (I'm not sure is this is right) / yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy --> second monomer ---------- --> alignment of extra dna residues (I'm not sure is this is right) * >P1; my_template hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh --> first monomer ---------- --> alignment of extra dna residues (I'm not sure is this is right) / kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk ---> second monomer ---------- --->alignment of extra dna residues (I'm not sure is this is right) / ---------------------------------------------------- ---> 1st strand of DNA ............. / ---------------------------------------------------- ---> 2nd strand of DNA ............. * Modeller worked without any warning but my dimer pass through the DNA molecule, so this is not working. Any help would be very appreciated. Sergio -- 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

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error message while ploting DOPE score
by hari krishna 24 Jan '11

24 Jan '11

Hi, i need help regarding the error that i'm getting while modeling protein. i have the ploting values from evaluate model and template. and i'm attempting to plot those value, but i'm getting error message: File "plot_profiles.py", line 1, in ? import pylab Importerror: No module named pylab could you please help to overcome this problem. -- *Thanks & regards* *N.Harikrishna,*

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Regarding Salign
by Ashish Runthala 21 Jan '11

21 Jan '11

I checked salign too. It considers penalties on primary sequence and then moves to the structural alignment of considered structures before adding target sequence according to generated structural topology. But will you pass me the script lines which aligns structures at 1,2,3,4Angstroms. My another doubt is that how the considered structures are considered all together for each of these distance cutoffs. Is this like nC2 combination based structural alignment satisfaction of restraint matrix generated. Show me where these 1,2,3,4 Angstroms are available in salign_iterative. I couldn't find them. Thanks, Ashish

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