November 2004 - modeller_usage

Helix Packing:Docking?
by David Piper 05 Nov '04

05 Nov '04

Modellers, I would like to add a single helix to an existing model. I have a set of distance restraints to orient residues on the helix to be added to the existing model. What sort of approach might be recommended here? Should I simply build a the additional helix ab initio, and then remodel the existing model + added helix based on the existing model + the built helix and distance restraints? Is there a way to simply add the new helix to the existing model by addition + distance restraints? Thanks, David

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Merge twp alignment files
by HYUN CHUL KIM 04 Nov '04

04 Nov '04

Hi, all I made two alignment files with a threading program other than MODELLER. How can I merge these two alignment files? Each alignment file containts one query sequence and one template sequence. Query sequences from two alignment files are same to each other and have different gaps. Following sequences and gaps are made randomly. file1: 1aaab.ali >P1;source sequence: query : 1: : 700: : target sequence: unknown: : MASNMLDS--------KFLDKLDFJLSDKFLKDFLSJFDLJFLKDJFLDKFLS* >P1;1aaab structure: 1aaab: 100: B : 800: B: template: known structure: : M-ASDFSAFDSADFSAFSDFSADFSAFSAD--ASDFASFDSAD--------* file2: 1bbbc.ali >P1;source sequence: query : 1: : 700: : target sequence: unknown: : MASNMLDSKFLDKLDFJLSDKFLKD----------FLSJFDLJFLKDJFLDKFLS* >P1;1bbbc structure: 1bbbc : 40: C : 700: C : template: known structure: : M-ASDFSAFDSADFSAFSDFSADFSAFSAD--ASDFASFDSAD----------* ******MY TARGET ALIGNMENT FORM********************* >P1;source sequence: query : 1: : 700: : target sequence: unknown: : MASNMLDSKF---LDKLDFJLSDKFLKD--FLSJFDLJFLKDJFLDKFLS* >P1;1aaab structure: 1aaab: 100: B : 800: B: template: known structure: : M-ASDFSAFDSADFSAFSDFSADFSAFSAD--ASDFASFDSAD-----* >P1;1bbbc structure: 1bbbc : 40: C : 700: C : template: known structure: : M-ASDFSAFDSADFSAFSDFSADFSAFSAD--ASDFASFDS-----AD* ****************************************************** Sincerely, Kim

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Unknown residue type,position,sequence......
by 서주현 04 Nov '04

04 Nov '04

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RE: [modeller_usage] Frustrating simple problem!
by Joel Tyndall 01 Nov '04

01 Nov '04

Hi folks, added to the errors pointed out by asmat (thanks for that), there was a break in the protein chain which I hadn't picked up. Thanks Joel -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Ph +64 3 4797293 Fax +64 3 4797034

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