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[求助] pymol视图软件里面氢键相关问题

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
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> -----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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