Dear users,
I am trying to produce a chimeric model for my protein. The first thing I want to do is to check the alignment I have.
When I tell Modeller to execute the "check_alignment" command, I get the following message:
rdpir___E> alignment sequence not found in PDB file: 1
./pXXXX.pdb
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The alignment I have is:
>P1;pXXXX
structureX:…
[View More]pXXXX:.::.:::::
CKPMSNFRF-GENHAIMGVAFTWVMALACAAPPLVGWS--RYIPEGMQC-SCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTH--------QGSDFGPIFMTIPAFFAKTSAVYNPVIYIMM*
>P1;pAveM
structure:pAveM:2::211:::::
-----------VRWAKLYSLVIWGCTLLLSSPMLV-----------------------------EVFTNMLLNVVGFLLPLSVITFCTMQ---------------------ERRATVLVLVVLLLFIICWLPFQISTFLDTL----------------VITQIASFMAYSNSCLNPLVYVIV*
>P1;Ali2
sequence:Ali2::::::::
VKTMSMGRMRGVRWAKLYSLVIWGCTLLLSSPMLVFRTMKEYSDEGHNVTACVISYPSL---IWEVFTNMLLNVVGFLLPLSVITFCTMQIMQVLRNNEMQKFKEIQT---ERRATVLVLVVLLLFIICWLPFQISTFLDTLHRLGILSSCQDERIIDVITQIASFMAYSNSCLNPLVYVIV*
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Perhaps, something is wrong with file names or PDB codes.(I stored the pdb files as pXXXX.pdb)
Can somebody help me?
Thank you very much,
Paola
--
dott. Paola D'Alessio (PhD student)
Universita' degli Studi di Salerno
Dipartimento Scienze Farmaceutiche
via Ponte Don Melillo, 84084 Fisciano (Sa), Italy
tel.+39 089 962822; e-mail: pdalessio(a)unisa.it
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I need help
by A.Romani＠leonardo.biomed.unipr.it
10 Sep '98
10 Sep '98
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I'm able to perform the basics of building, but now I've few questions to improve my model.
I'built the model with the top script below :
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INCLUDE # Include the predefined TOP routines
SET ALNFILE = 'alignment.ali' # alignment filename
SET SEQUENCE = 'my_sequence'
SET LIBRARY_SCHEDULE = 1
SET MD_LEVEL = 'refine1'
SET FINAL_MALIGN3D = 1
SET REPEAT_OPTIMIZATION = 5
SET RSTRS_REFINED = 5
SET MD_RETURN = '…
[View More]MINIMAL'
SET KNOWNS = 'knows1' 'knows2' 'knows3' # codes of the templates
SET ATOM_FILES_DIRECTORY = '/disk2/modeller4/examples' # directories for input atom files
SET STARTING_MODEL= 1 # index of the first model
SET ENDING_MODEL = 20 # index of the last model
# (determines how many models to calculate)
CALL ROUTINE = 'model' # do homology modelling
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With this script am I sure to build an accurate model? Are there other stuff that I can do to improve my
model? How can I transfer the heteroatoms from template to model?
Thanking in advance
Your faithfully
Antonello Romani
________________________________
Antonello Romani
Istituto di Patologia Generale
Plesso Biotecnologico Integrato
Universita' degli Studi di Parma
via Volturno 39
43100 Parma
Tel. +39 521 903 751
Fax. +39 521 903 742
E-mail : A.Romani(a)leonardo.biomed.unipr.it
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