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开心欢乐金虫 (正式写手)
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[求助]
pymol视图软件里面氢键相关问题
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下面是在一个帖子上看到的，关于pymol氢键的相关回复，原帖见 http://muchong.com/bbs/viewthread.php?tid=5472481 RE: [PyMOL] polar contact definition Warren DeLano Mon, 23 May 2005 20:36:20 -0700 Sergio, We use the term "polar contacts" because, as you correctly point out, some of the contacts shown don't meet strict hydrogen-bonding criteria. Of course, many macromolecular crystal structures aren't of high enough resolution to make definitive determinations anyway...so...With ideal geometry, PyMOL will show polar contacts out to:set h_bond_cutoff_center, 3.6 With minimally acceptable geometry, PyMOL will show polar contacts out to set h_bond_cutoff_edge, 3.2 These settings can be changed *before* running the detection process (dist command mode=2 or via the menus). Note that the hydrogen bond geometric criteria used in PyMOL was designed to emulate that used by DSSP. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz650)-872-0942 Tech650)-872-0834 . Fax650)-872-0273 Cell650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [ mailto:pymol-users-ad...@lists.sourceforge.net ] On Behalf Of > Sergio E. Wong > Sent: Monday, May 23, 2005 7:13 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] polar contact definition > > Dear Pymol users: > > I'm using pymol to find "polar contacts". I'm wondering what is the definition of a "polar contact". Some of the distances are longer than expected for a hydrogen bond. So, I'm left wondering what is the distance cut off employed. > Thanks > > -Sergio 我的问题： set h_bond_cutoff_center, 3.6 set h_bond_cutoff_edge, 3.2 这两个阈值的设定没看明白是什么？ 还有作者回复中最后提到Note that the hydrogen bond geometric criteria used in PyMOL was designed to emulate that used by DSSP. 是说pymol所显示的氢键其定义与DSSP所应用的氢键定义是一样的吗？ |
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