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*
#######################################################################################################################################
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 have been doing structural studies on various eye lens crystallins by
homology modelling using modeller 4. I have some queries in this regard.
1.The final models have no residues in the disallowed region of the
Ramachandaran plot as well as there are no bad contacts. Is this
evaluation enough for structure verification?
2. I want to mutate one residue in these models and I have gone thru the
top files for mutation. For reasons unknown to me, I could not use it
correctly. Besides the file …
[View More]needs the name of the residue to be mutated
and the one to be inserted instead but not the position. If the specific
name is given, all residues of the same name gets mutated.
3. The other important studies that I want to carry out is the effect of
sugar binding to the structure as well as binding of the small molucules
like phosphate, cyanate etc. I used Web lab Viewer Pro version to paste
and connect the small mol. to my protein.When I cleaned the entire
structure using "clean structure" command in Web lab, it leaves so many
bad contacts and many residues in the disallowed region of the
Ramachandaran plot.
So I decided to use the molecular dynamics and energy minimization by
MODELLER. The topology files do not have these small molecules in the
list. So it leaves the structure to be more disturbed.
Can you make the topology files if specified or can you help me sort out
how to make one?
Well these are so many questions! Can you please suggest something.
Thanks
asmat salim
HEJ Res Inst of Chem
Univ of Karachi
Pakistan
PS:How can I join your mailing list?
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I generated several loop conformations using the 'loop'
routine. The top file is similar to example 3 of the manual, with
the addition of gemetrical constraints on the end of loops.
I am refining 20 a.a. out of a 27-loop segment.
The refined loop conformations still have residues
located in unfavorable regions of the phi/psi plot, i.e. phi> 0 (non
Gly, or Asn). Typically, there are 1-4 residues in these regions.
Only 2% of my conformations have all residues with phi<0.
Are such …
[View More]occurrencies typical of the refinement procedure? If not,
how can I prevent this for happening?
Thanks
Germana
Germana Paterlini
Dept. of Medicinal Chemistry
Minneapolis, MN 55455
germana1(a)vwl.medc.umn.edu
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