- modeller_usage - salilab.org

Regarding alignment
by Ashish Runthala 21 Apr '11

21 Apr '11

Dear MODELLERS, MODELLER doesn't incorporate MSP based alignment consideration. I have two queries. 1. How to make MODELLER consider HSP to be extended on either side to generate. 2. How to generate a profile based best structural alignment of all considered templates against the target sequence. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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How to run flexEM package parallel
by ruiz＠berkeley.edu 20 Apr '11

20 Apr '11

Hi, Ben, I am using the flexEM package in modeller to refine a large complex. However, it took a long time for one CG/MD cycle. I wonder can I run the job in parallel ? Maybe you can directly edit the script below. Thanks! Rui # ============================================================================ # # a. Define the type of oprimization: conjugate gradients minimization (CG) # or molecular dynamics (MD) # b. Edit input parameters: density map parameters and probe structure # # ======================= Maya Topf, 4 Dec 2007 ============================= from modeller import * import shutil import sys, os, os.path import string import math from CG import opt_cg from MD import opt_md env = environ() ############### INPUT PARAMETERS ################## optimization = 'MD' # type of optimization: CG / MD rigid_filename = 'rigid.txt' # rigid bodies file name path = './' # directory path code = '1ake' # 4 letter code of the structure input_pdb_file = '1ake_init.pdb' # input model for optimization em_map_file = '1ake_10A.mrc' # name of EM density map (mrc) format='MRC' # map format: MRC or XPLOR apix=1.0 # voxel size: A/pixel box_size=69 # size of the density map (cubic) resolution=10.0 # resolution x=-9.0; y=14.0; z=-8.0 # origin of the map num_of_runs = 1 # number of runs initial_dir = 1 ############### RUN OPTIMIZATION ################## # CG # ---- if optimization == 'CG': for i in range(initial_dir,initial_dir+num_of_runs): scratch = path + '/' + str(i) + '/' os.system("mkdir -p " + scratch) os.system("cp " + path + '/'+ input_pdb_file + " " + scratch) os.chdir(scratch) opt_cg(path, code, str(i), 55*i, em_map_file, input_pdb_file, format, apix, box_size, resolution, x, y, z, rigid_filename) # MD # ---- elif optimization == 'MD': for i in range(initial_dir,initial_dir+num_of_runs): scratch = path + '/' + str(i) + '/' # input_pdb_file = 'final' + str(i) + '_cg.pdb' # os.chdir(scratch) opt_md(path, code, str(i), 10*i, em_map_file, input_pdb_file, format, apix, box_size, resolution, x, y, z, rigid_filename)

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restrict salign to subparts of some structures sequences
by Benjamin SCHWARZ 20 Apr '11

20 Apr '11

Hello modellers, I have a very large dataset of (beta propeller domain) structures, which I inspected visually to assess parts that sounded obviously not relevant for a structural alignment. For some structures I spotted long loops or several small helices insertions which I would like salign not to consider during the structural alignment. Is there a way to do so ? thanks --Ben.S

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Re: [modeller_usage] Long loop modeling
by bharat lal 20 Apr '11

20 Apr '11

Hi, I want to know whether long loop modeling of 30 or 40 residue length is possible through modeller or not ??.. ---------- Bharat

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 73
by Ashish Runthala 20 Apr '11

20 Apr '11

Dear Ramana, There is a script optimize.py. But MD+SA is already working. You won't get contrasting significant better model decoy. Run MODELLER for longer run to select decoy as per 3D-Jury or any other clustering method. Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Wednesday, April 20, 2011 2:50:13 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 73 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: Long loop modeling (bharat lal) 2. restrict salign to subparts of some structures sequences (Benjamin SCHWARZ) 3. How to run flexEM package parallel (ruiz(a)berkeley.edu) 4. (no subject) (rjayashree13-science(a)yahoo.co.in) ---------------------------------------------------------------------- Message: 1 Date: Fri, 15 Apr 2011 19:06:26 +0530 (IST) From: bharat lal <monu46010(a)yahoo.com> Subject: Re: [modeller_usage] Long loop modeling To: modeller <modeller_usage(a)salilab.org> Message-ID: <650005.60727.qm(a)web94712.mail.in2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" Hi, I want ?to know whether long loop modeling of 30 or 40 residue length is possible through modeller or not ??.. ----------? Bharat

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(no subject)
by rjayashree13-science＠yahoo.co.in 20 Apr '11

20 Apr '11

I have developed my homology models. wish to know how can I perform energy minimisation in Modeller? Dr. Jayashree Ramana

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(no subject)
by rjayashree13-science＠yahoo.co.in 14 Apr '11

14 Apr '11

I have a problem in which I am modelling a protein as a homodimer for which I am using a homodimeric template with ligands bound. When I model without ligand, it runs fine. But when I want to include heteroatoms, it says 'Number of residues between alignment and pdb file are different'. This is my script file. # Homology modeling by the automodel class from modeller import * # Load standard Modeller classes 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 env.io.hetatm = True # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] a = automodel(env, alnfile = 'mockali.ali', # alignment filename knowns = '1COD', # codes of the templates sequence = 'targetfile', # code of the target assess_methods=(assess.DOPE, assess.GA341)) 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 the actual homology modeling This is my alignment file. >P1 sequence::::: AAAAAAAAAAA/. BBBBBBBBBBB/.* >P1 structureX:::: AAAAAAAAAAA/. BBBBBBBBBBB/.* Dr. Jayashree Ramana

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 69
by Ashish Runthala 14 Apr '11

14 Apr '11

Respected Sir Benn, You didn't tell me the Alignment Score formula. Please share that. And you didn't tell me the utility of such a score, which looses its significance mostly, without being parallel to correct template selection/Model Accuracy. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Wednesday, April 13, 2011 8:26:21 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 69 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: How Alignment Score is calculated. (Modeller Caretaker) 2. modifiable version of salign.iterative_structural_align() (Benjamin SCHWARZ) 3. Re: modifiable version of salign.iterative_structural_align() (Modeller Caretaker) 4. Modelling a protein loop close to DNA ..... (Sergio Garay) ---------------------------------------------------------------------- Message: 1 Date: Mon, 11 Apr 2011 10:16:57 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] How Alignment Score is calculated. To: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Cc: modeller <modeller_usage(a)salilab.org> Message-ID: <4DA33789.70601(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 04/09/2011 10:00 PM, Ashish Runthala wrote: > When pairwise alignment score calculated by MODELLER > is not parallel to the Model Accuracy. Then what is the benefit > Alignment Score holds for? Benn, will you please tell me the formula > for calculating Alignment Score for a pairwise alignment. What is the > matrix it uses for alignment and score computation. How it is > calculated. The alignment score is simply the sum of residue-residue distances and gap penalties from tracing the path that dynamic programming finds through the alignment matrix. In general, alignment scores are a poor predictor of model quality. I'm not aware of any claims to the contrary in the Modeller documentation. 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: Tue, 12 Apr 2011 16:27:40 +0200 From: Benjamin SCHWARZ <schwarz.ben(a)gmail.com> Subject: [modeller_usage] modifiable version of salign.iterative_structural_align() To: modeller <modeller_usage(a)salilab.org> Message-ID: <4849E83D-7DA7-4A04-B74C-353FFB7E3453(a)gmail.com> Content-Type: text/plain; charset=us-ascii Hi list, If I understand well, the salign.iterative_structural_align() function is an exact implementation of the algorithm presented in [Madhusudhan2009]. Is there a python script version of this function ? Something that could be tweaked and modified... --Ben.S ------------------------------ Message: 3 Date: Tue, 12 Apr 2011 09:11:00 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] modifiable version of salign.iterative_structural_align() To: Benjamin SCHWARZ <schwarz.ben(a)gmail.com> Cc: modeller <modeller_usage(a)salilab.org> Message-ID: <4DA47994.8030108(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/12/11 7:27 AM, Benjamin SCHWARZ wrote: > If I understand well, the salign.iterative_structural_align() > function is an exact implementation of the algorithm presented in > [Madhusudhan2009]. Is there a python script version of this function > ? Something that could be tweaked and modified... Of course - all the Modeller scripts are Python scripts, so you can modify them to your heart's content. Look at modlib/modeller/salign.py. 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: Wed, 13 Apr 2011 07:09:59 -0400 From: Sergio Garay <sergio.alberto.garay(a)gmail.com> Subject: [modeller_usage] Modelling a protein loop close to DNA ..... To: modeller_usage(a)salilab.org Message-ID: <BANLkTimgaTV=x3+1BjjN3wq219UUsEGGvQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi all I have obtained a reasonably good model of protein dimer close to a DNA molecule just copying the DNA template into my target. But now I want to refine a protein loop close to DNA molecule but taking into account all "real" interactions between the atoms of my protein and DNA. At the moment I was not able to make modeller to recognize my target dna bases. So, my question is: if the ordering of the DNA base atoms in my pdb record are different to the one in top_heav.lib, Should I change it in my pdb or Should I rewrite the top in order to it matches with that of pdb file. Which method would be easier? . Below I paste a desoxi Gua from top_heav.lib (left) and a Gua residue from my template pdb in order to show the differences (right): RESI DGUA -1.00000 ATOM P P 1.50000 // ATOM 37 P DG A 3 49.258 12.669 8.835 ATOM OP1 ON3 -0.80000 // ATOM 38 OP1 DG A 3 48.625 13.322 7.669 ATOM OP2 ON3 -0.80000 // ATOM 39 OP2 DG A 3 49.792 11.303 8.659 ATOM O5' ON2 -0.55000 // ATOM 40 O5' DG A 3 50.393 13.597 9.434 ATOM C5' CN8 0.10000 // ATOM 41 C5' DG A 3 50.007 14.836 10.056 ATOM C4' CN6 0.20000 // ATOM 42 C4' DG A 3 50.897 15.123 11.268 ATOM O4' ON6 -0.40000 // ATOM 43 O4' DG A 3 50.655 14.196 12.319 ATOM C1' CN6B 0.20000 // ATOM 44 C3' DG A 3 52.366 15.009 10.907 ATOM N9 NN2 -0.14000 // ATOM 45 O3' DG A 3 53.017 15.983 11.686 ATOM C4 CN5 0.14000 // ATOM 46 C2' DG A 3 52.724 13.583 11.293 ATOM N3 NN3A -0.66000 // ATOM 47 C1' DG A 3 51.785 13.331 12.470 ATOM C2 CN2 0.76000 // ATOM 48 N9 DG A 3 51.356 11.909 12.533 ATOM N1 NN2G -0.10000 // ATOM 49 C4 DG A 3 51.166 11.181 13.676 ATOM N2 NN1 0.00000 // ATOM 50 C8 DG A 3 51.170 11.020 11.508 ATOM C6 CN1 0.55000 // ATOM 51 N7 DG A 3 50.833 9.812 11.874 ATOM O6 ON1 -0.47000 // ATOM 52 C5 DG A 3 50.777 9.903 13.268 ATOM C5 CN5 -0.08000 // ATOM 53 C6 DG A 3 50.374 8.977 14.276 ATOM N7 NN4 -0.69000 // ATOM 54 O6 DG A 3 49.799 7.879 14.135 ATOM C8 CN4 0.69000 // ATOM 55 N1 DG A 3 50.574 9.420 15.560 ATOM C2' CN6C 0.00000 // ATOM 56 C2 DG A 3 51.068 10.663 15.839 ATOM C3' CN6 0.10000 // ATOM 57 N3 DG A 3 51.310 11.614 14.951 ATOM O3' ON2 -0.55000 // ATOM 58 N2 DG A 3 51.319 10.942 17.075 I also changed my alignment in order to the bases can be recognized: >P1; TCP16 sequence:TCP16:::::::0.00:0.00 tjltllljjjejle / tjltllljjjejle / TPKDRHLKIGGRDRRIRI-----PPSVAPQLFRLTKELGFKTDGETVSWLLQNAEPAIFA ATGHG / TPKDRHLKIGGRDRRIRI-----PPSVAPQLFRLTKELGFKTDGETVSWLLQNAEPAIFA ATGHG * >P1; TCP16 structureX:TCP16:1:A:148:D:::-1.00:-1.00 tjltllljjjejle / tjltllljjjejle / TPKDRHLKIGGRD-----RRIRIPPSVAPQLFRLTKELGFKTDGETVSWLLQNAEPAIFA ATGHG / TPKDRHLKIGGRD-----RRIRIPPSVAPQLFRLTKELGFKTDGETVSWLLQNAEPAIFA ATGHG * Below I also paste the python script that I've used in the modelling. May be someone can find any error o misleading command. # 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'] #env.io.hetatm = True # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms (necessary) class MyLoop(loopmodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['CZ:45:C'], at['O6:6:A']), mean=3.0, stdev=0.5)) rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['CZ:105:D'], at['O6:20:B']), mean=3.0, stdev=0.5)) # This routine picks the residues to be refined by loop modeling #def special_restraints(self, aln): def select_loop_atoms(self): #Two loops for refinement at the same time return selection(self.residue_range('44:C', '47:C'), self.residue_range('103:D', '106:D')) m = MyLoop(env, alnfile = 'align2.ali' , inimodel='TCP16.B99990001.pdb', # initial model of the target sequence='TCP16') # code of the target m.loop.starting_model= 1 # index of the first loop model m.loop.ending_model = 1 # index of the last loop model m.loop.md_level = refine.very_slow # loop refinement method m.make() Any help or advice will be very appreciated. Sergio -- Sergio Garay Dr. en Ciencias Biol?gicas Facultad de Bioquimica y Cs. Biol?gicas 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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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 69
by Ashish Runthala 14 Apr '11

14 Apr '11

Dear SCHWARZ, Salign alterations won't help much, as such all the times. Some improvements in TBM-HA modeling can be achieved with some alteration of few parameters as the best set applied, over the default MODELLER set of parameters, and that too only when you have enough coordinate information available for a target sequence. But if you think to change (heartly as Benn said), think of augmented improvement of each parameter with the another alteration. Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Wednesday, April 13, 2011 8:26:21 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 69 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: How Alignment Score is calculated. (Modeller Caretaker) 2. modifiable version of salign.iterative_structural_align() (Benjamin SCHWARZ) 3. Re: modifiable version of salign.iterative_structural_align() (Modeller Caretaker) 4. Modelling a protein loop close to DNA ..... (Sergio Garay) ---------------------------------------------------------------------- Message: 1 Date: Mon, 11 Apr 2011 10:16:57 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] How Alignment Score is calculated. To: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Cc: modeller <modeller_usage(a)salilab.org> Message-ID: <4DA33789.70601(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 04/09/2011 10:00 PM, Ashish Runthala wrote: > When pairwise alignment score calculated by MODELLER > is not parallel to the Model Accuracy. Then what is the benefit > Alignment Score holds for? Benn, will you please tell me the formula > for calculating Alignment Score for a pairwise alignment. What is the > matrix it uses for alignment and score computation. How it is > calculated. The alignment score is simply the sum of residue-residue distances and gap penalties from tracing the path that dynamic programming finds through the alignment matrix. In general, alignment scores are a poor predictor of model quality. I'm not aware of any claims to the contrary in the Modeller documentation. 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: Tue, 12 Apr 2011 16:27:40 +0200 From: Benjamin SCHWARZ <schwarz.ben(a)gmail.com> Subject: [modeller_usage] modifiable version of salign.iterative_structural_align() To: modeller <modeller_usage(a)salilab.org> Message-ID: <4849E83D-7DA7-4A04-B74C-353FFB7E3453(a)gmail.com> Content-Type: text/plain; charset=us-ascii Hi list, If I understand well, the salign.iterative_structural_align() function is an exact implementation of the algorithm presented in [Madhusudhan2009]. Is there a python script version of this function ? Something that could be tweaked and modified... --Ben.S ------------------------------ Message: 3 Date: Tue, 12 Apr 2011 09:11:00 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] modifiable version of salign.iterative_structural_align() To: Benjamin SCHWARZ <schwarz.ben(a)gmail.com> Cc: modeller <modeller_usage(a)salilab.org> Message-ID: <4DA47994.8030108(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/12/11 7:27 AM, Benjamin SCHWARZ wrote: > If I understand well, the salign.iterative_structural_align() > function is an exact implementation of the algorithm presented in > [Madhusudhan2009]. Is there a python script version of this function > ? Something that could be tweaked and modified... Of course - all the Modeller scripts are Python scripts, so you can modify them to your heart's content. Look at modlib/modeller/salign.py. 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: Wed, 13 Apr 2011 07:09:59 -0400 From: Sergio Garay <sergio.alberto.garay(a)gmail.com> Subject: [modeller_usage] Modelling a protein loop close to DNA ..... To: modeller_usage(a)salilab.org Message-ID: <BANLkTimgaTV=x3+1BjjN3wq219UUsEGGvQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi all I have obtained a reasonably good model of protein dimer close to a DNA molecule just copying the DNA template into my target. But now I want to refine a protein loop close to DNA molecule but taking into account all "real" interactions between the atoms of my protein and DNA. At the moment I was not able to make modeller to recognize my target dna bases. So, my question is: if the ordering of the DNA base atoms in my pdb record are different to the one in top_heav.lib, Should I change it in my pdb or Should I rewrite the top in order to it matches with that of pdb file. Which method would be easier? . Below I paste a desoxi Gua from top_heav.lib (left) and a Gua residue from my template pdb in order to show the differences (right): RESI DGUA -1.00000 ATOM P P 1.50000 // ATOM 37 P DG A 3 49.258 12.669 8.835 ATOM OP1 ON3 -0.80000 // ATOM 38 OP1 DG A 3 48.625 13.322 7.669 ATOM OP2 ON3 -0.80000 // ATOM 39 OP2 DG A 3 49.792 11.303 8.659 ATOM O5' ON2 -0.55000 // ATOM 40 O5' DG A 3 50.393 13.597 9.434 ATOM C5' CN8 0.10000 // ATOM 41 C5' DG A 3 50.007 14.836 10.056 ATOM C4' CN6 0.20000 // ATOM 42 C4' DG A 3 50.897 15.123 11.268 ATOM O4' ON6 -0.40000 // ATOM 43 O4' DG A 3 50.655 14.196 12.319 ATOM C1' CN6B 0.20000 // ATOM 44 C3' DG A 3 52.366 15.009 10.907 ATOM N9 NN2 -0.14000 // ATOM 45 O3' DG A 3 53.017 15.983 11.686 ATOM C4 CN5 0.14000 // ATOM 46 C2' DG A 3 52.724 13.583 11.293 ATOM N3 NN3A -0.66000 // ATOM 47 C1' DG A 3 51.785 13.331 12.470 ATOM C2 CN2 0.76000 // ATOM 48 N9 DG A 3 51.356 11.909 12.533 ATOM N1 NN2G -0.10000 // ATOM 49 C4 DG A 3 51.166 11.181 13.676 ATOM N2 NN1 0.00000 // ATOM 50 C8 DG A 3 51.170 11.020 11.508 ATOM C6 CN1 0.55000 // ATOM 51 N7 DG A 3 50.833 9.812 11.874 ATOM O6 ON1 -0.47000 // ATOM 52 C5 DG A 3 50.777 9.903 13.268 ATOM C5 CN5 -0.08000 // ATOM 53 C6 DG A 3 50.374 8.977 14.276 ATOM N7 NN4 -0.69000 // ATOM 54 O6 DG A 3 49.799 7.879 14.135 ATOM C8 CN4 0.69000 // ATOM 55 N1 DG A 3 50.574 9.420 15.560 ATOM C2' CN6C 0.00000 // ATOM 56 C2 DG A 3 51.068 10.663 15.839 ATOM C3' CN6 0.10000 // ATOM 57 N3 DG A 3 51.310 11.614 14.951 ATOM O3' ON2 -0.55000 // ATOM 58 N2 DG A 3 51.319 10.942 17.075 I also changed my alignment in order to the bases can be recognized: >P1; TCP16 sequence:TCP16:::::::0.00:0.00 tjltllljjjejle / tjltllljjjejle / TPKDRHLKIGGRDRRIRI-----PPSVAPQLFRLTKELGFKTDGETVSWLLQNAEPAIFA ATGHG / TPKDRHLKIGGRDRRIRI-----PPSVAPQLFRLTKELGFKTDGETVSWLLQNAEPAIFA ATGHG * >P1; TCP16 structureX:TCP16:1:A:148:D:::-1.00:-1.00 tjltllljjjejle / tjltllljjjejle / TPKDRHLKIGGRD-----RRIRIPPSVAPQLFRLTKELGFKTDGETVSWLLQNAEPAIFA ATGHG / TPKDRHLKIGGRD-----RRIRIPPSVAPQLFRLTKELGFKTDGETVSWLLQNAEPAIFA ATGHG * Below I also paste the python script that I've used in the modelling. May be someone can find any error o misleading command. # 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'] #env.io.hetatm = True # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms (necessary) class MyLoop(loopmodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['CZ:45:C'], at['O6:6:A']), mean=3.0, stdev=0.5)) rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['CZ:105:D'], at['O6:20:B']), mean=3.0, stdev=0.5)) # This routine picks the residues to be refined by loop modeling #def special_restraints(self, aln): def select_loop_atoms(self): #Two loops for refinement at the same time return selection(self.residue_range('44:C', '47:C'), self.residue_range('103:D', '106:D')) m = MyLoop(env, alnfile = 'align2.ali' , inimodel='TCP16.B99990001.pdb', # initial model of the target sequence='TCP16') # code of the target m.loop.starting_model= 1 # index of the first loop model m.loop.ending_model = 1 # index of the last loop model m.loop.md_level = refine.very_slow # loop refinement method m.make() Any help or advice will be very appreciated. Sergio -- Sergio Garay Dr. en Ciencias Biol?gicas Facultad de Bioquimica y Cs. Biol?gicas 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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Modelling a protein loop close to DNA .....
by Sergio Garay 13 Apr '11

13 Apr '11

Hi all I have obtained a reasonably good model of protein dimer close to a DNA molecule just copying the DNA template into my target. But now I want to refine a protein loop close to DNA molecule but taking into account all "real" interactions between the atoms of my protein and DNA. At the moment I was not able to make modeller to recognize my target dna bases. So, my question is: if the ordering of the DNA base atoms in my pdb record are different to the one in top_heav.lib, Should I change it in my pdb or Should I rewrite the top in order to it matches with that of pdb file. Which method would be easier? . Below I paste a desoxi Gua from top_heav.lib (left) and a Gua residue from my template pdb in order to show the differences (right): RESI DGUA -1.00000 ATOM P P 1.50000 // ATOM 37 P DG A 3 49.258 12.669 8.835 ATOM OP1 ON3 -0.80000 // ATOM 38 OP1 DG A 3 48.625 13.322 7.669 ATOM OP2 ON3 -0.80000 // ATOM 39 OP2 DG A 3 49.792 11.303 8.659 ATOM O5' ON2 -0.55000 // ATOM 40 O5' DG A 3 50.393 13.597 9.434 ATOM C5' CN8 0.10000 // ATOM 41 C5' DG A 3 50.007 14.836 10.056 ATOM C4' CN6 0.20000 // ATOM 42 C4' DG A 3 50.897 15.123 11.268 ATOM O4' ON6 -0.40000 // ATOM 43 O4' DG A 3 50.655 14.196 12.319 ATOM C1' CN6B 0.20000 // ATOM 44 C3' DG A 3 52.366 15.009 10.907 ATOM N9 NN2 -0.14000 // ATOM 45 O3' DG A 3 53.017 15.983 11.686 ATOM C4 CN5 0.14000 // ATOM 46 C2' DG A 3 52.724 13.583 11.293 ATOM N3 NN3A -0.66000 // ATOM 47 C1' DG A 3 51.785 13.331 12.470 ATOM C2 CN2 0.76000 // ATOM 48 N9 DG A 3 51.356 11.909 12.533 ATOM N1 NN2G -0.10000 // ATOM 49 C4 DG A 3 51.166 11.181 13.676 ATOM N2 NN1 0.00000 // ATOM 50 C8 DG A 3 51.170 11.020 11.508 ATOM C6 CN1 0.55000 // ATOM 51 N7 DG A 3 50.833 9.812 11.874 ATOM O6 ON1 -0.47000 // ATOM 52 C5 DG A 3 50.777 9.903 13.268 ATOM C5 CN5 -0.08000 // ATOM 53 C6 DG A 3 50.374 8.977 14.276 ATOM N7 NN4 -0.69000 // ATOM 54 O6 DG A 3 49.799 7.879 14.135 ATOM C8 CN4 0.69000 // ATOM 55 N1 DG A 3 50.574 9.420 15.560 ATOM C2' CN6C 0.00000 // ATOM 56 C2 DG A 3 51.068 10.663 15.839 ATOM C3' CN6 0.10000 // ATOM 57 N3 DG A 3 51.310 11.614 14.951 ATOM O3' ON2 -0.55000 // ATOM 58 N2 DG A 3 51.319 10.942 17.075 I also changed my alignment in order to the bases can be recognized: >P1; TCP16 sequence:TCP16:::::::0.00:0.00 tjltllljjjejle / tjltllljjjejle / TPKDRHLKIGGRDRRIRI-----PPSVAPQLFRLTKELGFKTDGETVSWLLQNAEPAIFA ATGHG / TPKDRHLKIGGRDRRIRI-----PPSVAPQLFRLTKELGFKTDGETVSWLLQNAEPAIFA ATGHG * >P1; TCP16 structureX:TCP16:1:A:148:D:::-1.00:-1.00 tjltllljjjejle / tjltllljjjejle / TPKDRHLKIGGRD-----RRIRIPPSVAPQLFRLTKELGFKTDGETVSWLLQNAEPAIFA ATGHG / TPKDRHLKIGGRD-----RRIRIPPSVAPQLFRLTKELGFKTDGETVSWLLQNAEPAIFA ATGHG * Below I also paste the python script that I've used in the modelling. May be someone can find any error o misleading command. # 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'] #env.io.hetatm = True # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms (necessary) class MyLoop(loopmodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['CZ:45:C'], at['O6:6:A']), mean=3.0, stdev=0.5)) rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['CZ:105:D'], at['O6:20:B']), mean=3.0, stdev=0.5)) # This routine picks the residues to be refined by loop modeling #def special_restraints(self, aln): def select_loop_atoms(self): #Two loops for refinement at the same time return selection(self.residue_range('44:C', '47:C'), self.residue_range('103:D', '106:D')) m = MyLoop(env, alnfile = 'align2.ali' , inimodel='TCP16.B99990001.pdb', # initial model of the target sequence='TCP16') # code of the target m.loop.starting_model= 1 # index of the first loop model m.loop.ending_model = 1 # index of the last loop model m.loop.md_level = refine.very_slow # loop refinement method m.make() Any help or advice will 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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