November 1999 - modeller_usage

problem!
by Paola D'Alessio 15 Jun '01

15 Jun '01

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 ####################################################################################################################################### The alignment I have is: >P1;pXXXX structureX: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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queries
by Dr Ahsan Salim 29 Nov '99

29 Nov '99

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 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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loop refinement
by M. Germana Paterlini 10 Nov '99

10 Nov '99

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 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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