- modeller_usage - salilab.org

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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modifiable version of salign.iterative_structural_align()
by Benjamin SCHWARZ 12 Apr '11

12 Apr '11

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

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How Alignment Score is calculated.
by Ashish Runthala 11 Apr '11

11 Apr '11

Dear MODELLERS, 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. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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homodimer problem
by rjayashree13-science＠yahoo.co.in 11 Apr '11

11 Apr '11

My template is a homodimer and I want to model my target also as a hmodimer. The sequence of the chain A of homodimer in the PDB file is like: MKQA.............G. The sequence of the chain B of homodimer in the PDB file is like: MKQA.............GK. The sequence of protein in the NCBI protein database is like: MKQA.............GK. I have studied how to model a protein as a dimer using modeller (http://salilab.org/archives/modeller_usage/2010/msg00273.html) But if there is a slight difference in the two chains, like in this case the K residue is extra, then what should I do? (It would show a sequence difference if I use chain copy the same alignment in both) Please suggest.

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MSE query
by rjayashree13-science＠yahoo.co.in 09 Apr '11

09 Apr '11

I have a question about selenomethionine residues in PDB file. In the original sequence file, these are methionine residues but in PDB these are selenomethionine. I am using this PDB structure as a template. Can you suggest what is to be done about these residues? R Jayashree

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salign multiple structures, with an initial multiple sequence alignment
by Benjamin SCHWARZ 08 Apr '11

08 Apr '11

Hi Modellers, Trying to align several structures of a similar domain, I have a "hand-made" sequence alignment for these domains. Is it possible to ask salign to use this initial sequence alignment ? Is it possible to ask salign to keep that same multiple sequence alignment unchanged during the whole process ? thanks --Ben.S

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can salign output a "structural mapping" of residues
by Benjamin SCHWARZ 08 Apr '11

08 Apr '11

As a first (naive) question on that mailing list, I wonder if (and how) it is possible to retrieve residues that are structurally aligned as a result of a aln.salign() run (object aln being of type alignment). To precise my question, I know a (multiple) sequence alignment is produced as a result of this salign command and can be output with aln.write(), but I am more concerned by the possible mapping of residues in the structural alignment, that might not be apparent in the sequence. --Ben.S

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IS SCWRL4 helpful for Models
by Ashish Runthala 07 Apr '11

07 Apr '11

MODELLER9v9 models couldn't be improved further with SCWRL4. There was no difference in the GDT, TM_Score and RMSD statistics of model with and without SCWRL usage. So are all the side chain rotamer loci best optimized with the Calpha atom topologies? Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Re: [modeller_usage] How to get Secondary Structure in Alignment file
by Thomas Evangelidis 06 Apr '11

06 Apr '11

Dear Ashish, Thomas, > I don't expect all this what you replied. > > See i understand all that what you told. But there is a big problem there, > to try multiple alignments and iterated trials to land on good models(which > itself is ambiguous, as you can't really discriminate good and bad model, > until you have answer or GDT). > Two important factors influence the ability to predict accurate models: the extent of structural conservation between target and template, and the correctness of alignment (Kryshtafovych et al 2005, PMID: 16187365). The alternative alignments serve as a means to optimize the alignment at regions of sparse sequence similarity, which usually do not include common SSEs. Apart from statistical potentials and protein geometry checks, I'm not aware of any other method to discriminate good and bad structures. > So i am developing a complete in-house algorithm to result in the best > representative alignment from > the considered templates against the target. So i want to incorporate > secondary structure information or localized fold topologies to generate a > 3D alignment file. Hence i am looking forward for a python script which can > be integrated with MODELLER to result in the information like this. > > Template1> HCLCH > Template2> HCLHH > Target> xxxxx > (H=Helix. C=Coil, L=Loop) > > I JUST NEED SECONDARY STRUCTURE INFORMATION OF EACH ALIGNED RESIDUE OF EACH > TEMPLATE, BASED ON ITS PROBABILITY TO LAND IN SAME FOLD, AS PER THE > AVAILABLE PROXIMAL RESIDUES. > > I'm not aware how you can get the sequence alignment in that form from MODELLER, but there must be a way perhaps with another program. Alternatively you can write a code snippet in python that will call PyMol or VMD to get the secondary structure of each residue of your templates (I can give you my scripts in case you are interested). > Ya, and by the way, SCRWL won't help if you choose bad template/alignment. > Refinement improves GDT_TS scores by just 4 or 5%. Good coordinate selection > is most important. MODELLER also can't result in good models, if you mix up > incorrect template informations, and the problem becomes more complex, when > the new fold comes up. > > I never said that. When sequence identity <35%, the rotamers of conserved residues may differ in up to 45% of the cases (Sanchez et al. 1997, PMID: 9485495 ). SCWRL4 is used upon optimum template(s) and alignment selection to optimize the rotamers. This approach has been also implemented by the best performing human-expert group in CASP8 (Venclovas et al 2009, PMID: 19639635). In essence, I use the alternative-alignment approach when I have to choose between templates that have 25-40% sequence identity with the target. Provided that all templates share the same fold (i.e. may belong to the same SCOP family or have high CE-MC mean *Z*-scores), the selection of multiple templates in that low sequence similarity level produces better models than those constructed from a single parent (Moult J 2005, PMID: 15939584; Dalton et al 2007, PMID: 17510171). HMOPAL (that's the name of my pipeline) aims to select the best template combination and alignment based on the native-likeness of the resulting homology models, as judged primarily by the DOPE-HR raw score, and secondarily by PROCHECK and WHATCHECK. regards, Thomas > Thanks for support. > Ashish > > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > > ----- Original Message ----- > From: "Thomas Evangelidis" <tevang3(a)gmail.com> > To: "Ashish Runthala" <ashishr(a)bits-pilani.ac.in> > Cc: "modeller usage" <modeller_usage(a)salilab.org> > Sent: Tuesday, March 29, 2011 4:46:20 AM GMT +05:30 Chennai, Kolkata, > Mumbai, New Delhi > Subject: Re: [modeller_usage] How to get Secondary Structure in Alignment > file > > > > > On 27 March 2011 10:05, Ashish Runthala < ashishr(a)bits-pilani.ac.in > > wrote: > > > Dear Thomas, > I will write it clearly this time. > Take simplest case.Suppose, I have a structural/sequence alignment of 3 > templates against a target sequence. Now, as modeller predicts tertiary > conformation for the target sequence, it surely predicts the alignment based > secondary structure information against all the templates. So now i want > that specific secondary structure information along with the alignment file > for the aligned templates against the target sequence. > Now my C script will take on this alignment file to generate the > representative best possible optimum alignment for the considered target > sequence. These models in my tried iterations for the CASP8 targets gave > excellent results. > > > So if I understand correctly, your script creates alternative alignments, > then runs Modeller to build a model of the target from each alignment, it > reads the secondary structure (SS) from each model, and based on this SS it > judges which alternative alignment is the optimum. Is this how it works? Can > you elaborate on the algorithm? What are the criteria to select the optimum > alignment and what is the answer you seek from the mailing list? > > > I think i made myself clear this time. > By the way, what you are working on. I think you are also working on the > same topics. What you have redefined? I am interested to know that. > > > I've been working on optimization at the alignment level in the past, but > in my approach the selection of the optimum alignment and template > combination is based on the overall native-likeness of the resulting > homology models, not just the secondary structure of the target. More > specifically, I create homology models at several levels of optimization and > refinement from alternative alignments and different template combinations. > The resulting models are sorted according to the DOPE-HR score, and the best > of them undergo side-chain optimization with SCWRL4, and extensive > stereochemical tests with the programs PROCHECK and WHAT_CHECK to select the > best of them. The whole procedure is streamlined and parallelized with a > combination of bash and python scripts. However, it has been tested only on > my cases and a few CASP9 targets. More details can be found at: > > https://sites.google.com/site/hmopalpipeline/home (I will update the > website tomorrow) > > > > > Thanks in advance, > > Ashish > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > > ----- Original Message ----- > From: "Thomas Evangelidis" < tevang3(a)gmail.com > > To: "Ashish Runthala" < ashishr(a)bits-pilani.ac.in > > > > > Cc: "modeller usage" < modeller_usage(a)salilab.org > > Sent: Saturday, March 26, 2011 6:06:02 PM GMT +05:30 Chennai, Kolkata, > Mumbai, New Delhi > Subject: Re: [modeller_usage] How to get Secondary Structure in Alignment > file > > > > On 26 March 2011 07:47, Ashish Runthala < ashishr(a)bits-pilani.ac.in > > wrote: > > > Dear Thomas, > You mentioned the free tools in details. I appreciate that. But what i > don't understand is to manually call everyone, and then keep on doing it, is > tedious but fun it is. > > > So if I get it right this time, you didn't ask what commercial free tools > are available to display your sequence alignment along with the secondary > structure, is that correct? Could you please be more careful with your > syntax cause it's kind of difficult to follow you. > > > I had a query that template secondary structure information is there in > templates, but with indels, that may be disturbed. I mean the native > information is deteriorated. > > So if based on indels, available in current alignment, if i can link > directly to a python script. So that my next programme to generate the > optimal alignment will become successful, as i did all of these several > times manually, to design the algorithm to generate best representative > alignment. > > > So you want to write a python script that can cope with indels inside SSEs. > Namely, given a structure-based alignment between your target and templates, > you want to select which of the following alignments is the optimum: > > target > HCSIHHSC > Template1> HCSIHISC > Template2> HCSHHISC > ------------------------------------------------------- > target > HCS-IHHSC > Template1> HCS-IHISC > Template2> HCSH-HISC > ------------------------------------------------------- > target > HCSI-HHSC > Template1> HCS-IHISC > Template2> HCS-HHISC > > etc. > > > Is this what you seek? > > > > > > > > Will you please elaborate this time. > > > Thanks, > Ashish > > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > > > > > ----- Original Message ----- > From: "Thomas Evangelidis" < tevang3(a)gmail.com > > To: "Ashish Runthala" < ashishr(a)bits-pilani.ac.in > > Cc: "modeller" < modeller_usage(a)salilab.org > > Sent: Friday, March 25, 2011 4:50:42 PM GMT +05:30 Chennai, Kolkata, > Mumbai, New Delhi > Subject: Re: [modeller_usage] How to get Secondary Structure in Alignment > file > > Maestro from Schrodinger can display both the predicted secondary structure > elements (SSE) of the target and the SSE of the templates above the > alignment dynamically (namely if you change the alignment the SSEs are > changed accordingly). > > Alternatively you can use the following commercial free tools: > > ESPript ( http://espript.ibcp.fr/ESPript/ESPript/ ): can create an image > of your alignment with the SSEs of your templates above it. No SSE of the > target is displayed though. > > MolIDE ( http://dunbrack.fccc.edu/molide/index.php ): I have the notion > that this alignment editor (and not only) can display both the predicted SSE > of the target and the SSE of the templates. However, I didn't manage to run > it yet due to compilation problems. I intend to give it a try in the near > future. > > STRAP ( http://3d-alignment.eu/ ): it can do both but the GUI is not handy > in Linux (windows and fonts are unequal, etc.). > > Finally you can add a row with the secondary structure (as you wrote it in > your email) above each sequence in your alignment editor. I prefer Jalview > and like to play around with groups and colors. See the attached image for > an example. SSE of your templates can be retrieved from PDB (e.g. > http://www.pdb.org/pdb/explore/sequenceText.do?structureId=2IXF&chainId=A) whereas the SSE of your target can be predicted by Jpred3 ( > http://www.compbio.dundee.ac.uk/www-jpred/ ). > > > HTH, > > Thomas > > > > > On 25 March 2011 05:47, Ashish Runthala < ashishr(a)bits-pilani.ac.in > > wrote: > > > Dear Modellers, > Suppose i have two templates, and a target sequence. Instead of sequence > alignment based file, i want to consider the secondary structure > information, like given below > > Template1> HCSIHISC > Template2> HCSHHISC > > H=Helix, C=Coil, S-Strand, I=Indels > > Is it possible to get the alignment in this case for multiple templates > against the target sequence( whose structure can also be represented as best > aligned folds) > > Thanks > Ashish > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > > > > -- > > > ====================================================================== > > Thomas Evangelidis > > PhD student > > Biomedical Research Foundation, Academy of Athens > > 4 Soranou Ephessiou , 115 27 Athens, Greece > > email: tevang(a)bioacademy.gr > > tevang3(a)gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > > > > -- > > > ====================================================================== > > Thomas Evangelidis > > PhD student > > Biomedical Research Foundation, Academy of Athens > > 4 Soranou Ephessiou , 115 27 Athens, Greece > > email: tevang(a)bioacademy.gr > > tevang3(a)gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > > > > -- > > > ====================================================================== > > Thomas Evangelidis > > PhD student > > Biomedical Research Foundation, Academy of Athens > > 4 Soranou Ephessiou , 115 27 Athens, Greece > > email: tevang(a)bioacademy.gr > > tevang3(a)gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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