December 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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(no subject)
by Dermot Mallon 02 Jan '14

02 Jan '14

<<apologies for duplicate - I hit 'send' by mistake''>> Dear all, I have a large number of homology models to produce which have ~90 - 95% homology with 10 high quality crystal structure templates. Once I create my models I will be using GROMACS to relax the structure before comparing various properties of the models. I wonder, is it a reasonable approach to energy minimize the templates and use these as templates for producing models thereby reducing the need for energy minimization on (a much larger number of) models? Your opinion would be appreciated. Best wishes, Dermot

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Exclude residues from modeling
by Jurgens de Bruin 02 Jan '14

02 Jan '14

Hi, I would like to know what would be the best option to exclude residues from the N and C terminal of the target. The sequence can be truncated in the fasta file before modelling I believe would be the easy answer but does MODDELLER have a option/function that would have this? Thanks -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin

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DOPE for multiple template-based homology modeling
by HERBERT MAX VENTHUR PE¥A 19 Dec '13

19 Dec '13

Hi... Recently, I performed homology modeling using multiple templates with success (following the advanced tutorial). However, I could not pick a specific structure because I didn't find a dope score into the log file. Is there any posibility to obtain this dope score for multiple templates-based models?. thanks a lot for your answers Best wishes Herbert -- *Herbert Venthur PeñaProfesor de Estado en Ciencias con Mención en Química* *Estudiante de Doctorado en Ciencias de Recursos Naturales* *Laboratorio de Química Ecológica* *Departamento de Ciencias Químicas y Recursos Naturales* *Universidad de La FronteraTemuco, Chile* *08-3104992*

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Energy minimization
by Dermot Mallon 19 Dec '13

19 Dec '13

Dear all, I have a large number of homology models to produce which have ~90 - 95% homology with 10 high quality crystal structure templates. Once I create my models I will be using GROMACS to relax the structure before comparing various properties of the models. I wonder, is it a reasonable approach to energy minimize the templates and use this

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Replacing cysteine with homocysteine
by Arjun Ray 16 Dec '13

16 Dec '13

Hi, I wanted to replace a specific cysteine residue with homocysteine. Has someone done a similar operation with Modeller? Could someone suggest a methodology or script to do so? Thanks in advance. Regards Arjun -- **************************************************** The dream is not that you see in sleep , dream is which does not let you sleep. ~Dr. Abdul Kalam (Former President of Republic of India) ***************************************************** Arjun Ray Mobile : +919910497608 Email : arjun(a)ebi.ac.uk / arjun(a)cbr.su.se <arjun.ray(a)cbr.su.se> ***********************************************

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Allhmodel chirality inversion
by gbanoczi＠mail.bme.hu 09 Dec '13

09 Dec '13

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TypeError: restraint_group should be a physical_type object
by Isaure Chauvot de Beauchene 05 Dec '13

05 Dec '13

Hi, I try to do homology modeling by the automodel class. I get this error: File "/usr/lib/modeller9.12/modlib/modeller/modeller/restraints.py", line 170, in make_distance raise TypeError("restraint_group should be a physical_type object") I used mod9.12 on Ubuntu 12.04 with python2.7, with those script and alignment 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 # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] a = automodel(env, alnfile = '1FLZ-WT-MU.ali', # alignment filename knowns = '1FLZ', # codes of the templates sequence = '1FLZ-H15Y-H206R') # code of the target 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 ***************************** >P1;1FLZ structureX:1FLZ: 5 :A:229 :A:undefined:undefined:-1.00:-1.00 LTWHDVLAEEKQQPHFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIA IPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLW GSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQHGETPIDWMPVLPAESE* >P1;1FLZ-H15Y-H206R sequence:1FLZ-H15Y-H206R: : : : ::: 0.00: 0.00 LTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIA IPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLW GSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPAESE* ***************************** Where could this error come from? Thanks a lot in advance, Isaure

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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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