发信人: tiangeng (田大榜), 信区: Biology
标 题: Re: What kind of software is goog for drawing secondary str
发信站: BBS 未名空间站 (Wed Nov 9 19:08:42 2005), 转信

我只知道用pymol（免费的）可以做helix和b－strand。
用这样一个script：
build-helix.pml
以下是script内容
set secondary_structure,1
editor.attach_amino_acid('pk1','ala')
editor.attach_amino_acid('pk1','ala')
editor.attach_amino_acid('pk1','ala')
editor.attach_amino_acid('pk1','ala')
editor.attach_amino_acid('pk1','ala')
editor.attach_amino_acid('pk1','ala')
editor.attach_amino_acid('pk1','ala')
editor.attach_amino_acid('pk1','ala')
editor.attach_amino_acid('pk1','ala')
editor.attach_amino_acid('pk1','ala')
save ala.pdb,(ala)
第一行定义结构是什么样的。
1:a-helix, 2:反平行b-strand, 3:平行b-strand
还没有研究出来pi helix和310 helix是什么符号或者能实现吗。
下面那些行。
是依次加入的氨基酸。你可以把ala换成任何你想加的。
最后一行是存这个生成的pdb文件。
我觉得这个一个序列折叠成什么样的结构更多还取决于它的环境。
单独看不大好看出来那种更稳定。
记得这个在某本生化书里讲过。一个序列可以在helix和strand下都稳定。
【 在 bluesnail (ff) 的大作中提到: 】
: I mean if I know a protein's primary structrure, like AlaAlaAlaAla, I want
to
: draw its possible 2nd sturctures like alpha helix, pai helix, 310 helix. so
I
: can figure out what is the difference among all these structures. because
: sometimes it favors this conformation, under some condition, if prefers
other
: conformation. like draw some molecuar structure, but chemical software I
know
: is not good to do this thing because of my big molecule.I wonder whether
some
: biological software is good at this. wish you can understand. Thank you
anyway
: .



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