November 2013 - modeller_usage

Select and remove atoms from automodel
by Ignacio Ibarra 04 Mar '14

04 Mar '14

Hello, Currently I am generating nucleic acid models using the MODELLER suite. I would like to remove the initial phosphate group declared in the first residue of each nucleic acid chain. Those atoms should not be present in real structures. I would like to do it without writing new text in the .lib files that are into the modlib folder I read about a pick_atoms() method in an older version of MODELLER, but it is not commented in the 9v11 manual ( http://binf.gmu.edu/software/MODELLER/node131.html) Is there something similar currently available for removing atoms from the model in the automodel or another class? Regards, Ignacio

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Question to the align2d_mult.py file
by Simone Fulle 05 Dec '13

05 Dec '13

Dear modeller team, I am using a variant of the align2d_mult.py script on your homepage. I want to use a multi-sequence alignment, align several template structures and the query sequence to it without changing the initial multi-sequence alignment. On the webpage it is mentioned that one can use align_block to fix a specific part of the alignment. Just to make sure - by using the script: #!/usr/bin/python from modeller import * log.verbose()#output=1, notes=1, warnings=1, errors=1, memory=0) env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') # Read aligned sequences: aln = alignment(env) aln.append(file='../alignments/test.pir', align_codes='all') aln_block = len(aln) # Read aligned structures: aln.append(file='../templates/pdb_fit/alignment_test_structures.ali', align_codes='all') # Structure sensitive variable gap penalty sequence-sequence alignment: aln.salign(output='', max_gap_length=20, gap_function=False, # to use structure-dependent gap penalty alignment_type='PAIRWISE', align_block=aln_block, feature_weights=(1., 0., 0., 0., 0., 0.), overhang=0, gap_penalties_1d=(-450, 0), gap_penalties_2d=(0.35, 1.2, 0.9, 1.2, 0.6, 8.6, 1.2, 0., 0.), similarity_flag=True) aln.write(file='../alignments/modeller_multi.ali', alignment_format='PIR') aln.check() --------------------------- where "alignment_test_structures.ali" contains an alignment of potential template structures; is each of the sequence in "alignment_test_structures.ali" independently aligned to the alignment given in "test.pir" without changing the "test.pir" alignment? Thanks in advance! Kind regards, Simone

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"No module named modeller"
by Cecilia Lindgren 05 Dec '13

05 Dec '13

Hi, I am completely new to Modeller. I am using Linux and have downloaded and installed the Linux(64-bit x86_64RPM) package, as recommended at the website. I have tried to run scripts from the basic tutorial, but keep getting the following error message: ImportError: No module named modeller I have been trying to include the path to modeller in PATH, but have not succeeded. I have python2.7.6 installed. I would be very grateful if anyone have any ideas of what I can try! Best regards, Cecilia

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mutate_model on protein with ligand
by Anna Marabotti 18 Nov '13

18 Nov '13

Dear Modeller caretaker, I used mutate_model.py to introduce a single point mutation into the structure of my protein with a ligand bound into the active site. The mutation I introduced was near the ligand, and when I had a look at the resulting structure, I saw that the mutated residue has been located in too strict proximity with the ligand (i.e. the mutated residue and the ligand collide with each other). My suspicion is that this script does not take into account the presence of ligands or other elements marked as HETATM in the original protein. Is this true? In order to encompass this problem, if this is true, can I simply replace HETATM with ATOM in order to make mutate_model.py correctly functioning? Many thanks in advance and best regards Anna Marabotti -- ______________________________________________ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Giovanni Paolo II, 132 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabotti(a)unisa.it Skype: annam1972 Web page: http://www.unisa.it/docenti/annamarabotti/index "Indifference is the eighth deadly sin" (don Andrea Gallo)

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Multiple models for a single template
by vigneshwari subramanian 15 Nov '13

15 Nov '13

Dear Modeller users, I am interested in creating models for 100 different targets based on a single template. Is there an easy way to do this in modeller? Thanks, vigneshwari

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How to improve sequence alignment?!
by Amjad Farooq 13 Nov '13

13 Nov '13

Hi everyone, I am noticing that Modeller does not do a good job when it comes to sequence alignment of short peptides or DNA sequences. For example, please see the the comparison below: (1) Modeller alignment: Template GTPPPP - - YTVG Peptide TVLPPPPYRHRN (1) ClustalW alignment: Template -GTPPPPYTVG- Peptide TVLPPPPYRHRN As you can see, Modeller is unable to align up properly the central PPPPY motif in my peptide with the template!! In contrast, ClustalW is spot on in its ability to recognize a key pattern in the sequence. Is there a way to improve sequence alignment in Modeller? How can I make changes to the following Modeler file that I am using for my sequence alignment: # Make a pairwise alignment of two sequences aln = alignment(env, file='template.ali') aln.salign(overhang=30, gap_penalties_1d=(-450, -50), alignment_type='tree', output='ALIGNMENT') aln.write(file='template.pir', alignment_format='PIR') aln.write(file='template.pap', alignment_format='PAP') What parameters or settings, if any, could be changed in the above setup to improve sequence alignment in Modeller? Thank you so much for your advice and any comments that you may have. *AMJAD FAROOQ PhD DIC | Associate ProfessorDept of Biochemistry & Molecular Biology | Miller School of Medicine | University of Miami | Miami | FL 33136Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami , FL 33136 amjad(a)farooqlab.net <amjad(a)farooqlab.net> | off 305-243-2429 | lab 305-243-9799 | fax 305-243-3955 | www.farooqlab.net <http://www.farooqlab.net>*

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help regarding some problems related to modelling
by DHWANI DHOLAKIA 12 Nov '13

12 Nov '13

Dear sir/mam I am Dhwani Dholakia Doing M.Tech from Delhi Technological University. I am Using advanced homology modelling for my project work but while doing pdb search i could not find much good E value or % identity or query coverage.. I am confused that should i use a invivo modelling software like I-TASSER or advanced modelling . And also if can help me with the threshold values of various parameters to be used for advanced homology modelling.. Thanking You -- Dhwani Dholakia M.Tech bioinformatics Delhi Technological University

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questions about multichains modeller
by Yi Kong 12 Nov '13

12 Nov '13

Dear colleagues, I have a problem in multichain modeller. according the template file in automodel folder, I created the input file and script file. however when I　run this script, I recieved warnings listed below. Who knows how to reslove the problem? Thanks a lot! You can find many useful example scripts in the examples\automodel directory. It is recommended that you use Python to run Modeller scripts. However, if you don't have Python installed, you can type 'mod9.12' to run them instead. d:\Program Files (x86)\Modeller9.12> d:\Program Files (x86)\Modeller9.12>cd examples d:\Program Files (x86)\Modeller9.12\examples>cd automodel d:\Program Files (x86)\Modeller9.12\examples\automodel>python model-multichain-d ec1.py > model-multichain-dec1.log Traceback (most recent call last): File "model-multichain-dec1.py", line 37, in <module> a.make() # do homology modeling File "d:\Program Files (x86)\Modeller9.12\modlib\modeller\automodel\automodel. py", line 96, in make self.homcsr(exit_stage) File "d:\Program Files (x86)\Modeller9.12\modlib\modeller\automodel\automodel. py", line 410, in homcsr aln = self.read_alignment() File "d:\Program Files (x86)\Modeller9.12\modlib\modeller\automodel\automodel. py", line 400, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "d:\Program Files (x86)\Modeller9.12\modlib\modeller\alignment.py", line 78, in append allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was n ot found in the alignment file; ALIGN_CODES( 1) = 4h10 d:\Program Files (x86)\Modeller9.12\examples\automodel>

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multiple templates - loop modelling
by Simone Fulle 08 Nov '13

08 Nov '13

Dear all, I would like to model a protein using two templates and (!) define which parts of the structure are modeled by which template. I.e. the core of the structure by template_1 and a specific loop by template_2. The template structures are already aligned. Any suggestions and comments will be highly appreciated. I am aware that I could generate a "Fused_template_structure" manually but it would be really nice if I could do it in an automatic fashion. Kind regards, Simone

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homology modelling
by pr＠tibh＠ 07 Nov '13

07 Nov '13

How can i build a homology model using template,my template is a crystal structure of a chimeric protein. though it has a 94% query coverage and 48% identity with my target sequence. sequence alignment of non chimeric protein as a whole is very much identical.Can i use the chimeric crystal structure for modelling?

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