modeller_usage

modeller_usage@salilab.org

3151 discussions

Missed residues
by James Starlight 16 Jan '14

16 Jan '14

Dear Modeller users, I used Modeller for creation of the Chimeric proteins (linked from C to N termi) consisted of merged two tempates. Below you can see my aligment file for such task. >P1;1gfl structureX:1gfl:1 ::238 : :::-1.00:-1.00 ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------* >P1;3u10 structureN:3u10:470 ::671 : :A::-1.00:-1.00 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILL* >P1;seq sequence:seq: : : : ::: 0.00: 0.00 ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYKDSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILL* I wounder to know if it possible to add to my resulted chimeric protein some missed residues (commonly in N, C termi and loops regions) which are absent in both templates .In the above example in first PDB template 1-5 residues from N- term are absent (this residues are not listed in aligment file too). Does it posible to add to the final model ? Please provide me with some examples where modeller is used for the addition of missed loops and termi. Thanks for help, James

2 1

Reg modeller
by Manjula Mummadisetti 08 Jan '14

08 Jan '14

I have a protein which has its N-terminal region missing from its cyrstal structure. On generating a model using modeller, it formed a loop at the N-terminus. I would like to try making an alpha helix and a beta sheet at the N-terminus in place of loop. In the addrsr file, I mentioned the residues which have to be used to form the alpha helix, but the modeller is giving an error message: syntax error. I am not sure what is going wrong. I just changed the residue numbers to the desired residues, and didn't change anything else in the script file. I am a new user, and I am a little stuck at this point. Any advice will be highly appreciated. Thanks

2 1

(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

2 1

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

2 1

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*

3 2

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

1 0

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> ***********************************************

2 1

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

09 Dec '13

2 1

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

2 1

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

2 1

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modeller_usage