[Chimera-users] question about Chimera
wuxue at nankai.edu.cn
Tue Sep 22 17:18:10 PDT 2009
Thank you very much for your instruction.
We'll follow your guide.
>From: Elaine Meng <meng at cgl.ucsf.edu>
>Reply-To: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
>To: 吴雪<wuxue at nankai.edu.cn>
>Subject: Re: [Chimera-users] question about Chimera
>Date: Tue, 22 Sep 2009 11:00:11 -0700
>Dear Wu Xue,
>There are several different distance and angle cutoffs that depend on
>the donor and acceptor atom types. For example, the distance and
>angle cutoffs for finding a H-bond donated from hydroxyl -OH to
>carbonyl =O will be different than from amine -NH3 to carbonyl =O.
>The cutoff values are taken from tables in this paper:
> Three-dimensional hydrogen-bond geometry and probability
>information from a crystal survey. Mills JE, Dean PM. J Comput Aided
>Mol Des. 1996 Dec;10(6):607-22.
>As discussed in the FindHBond documentation,
>the criteria in this paper were based on very high resolution crystal
>structures of small molecules. Typically the structures in the PDB
>are not so high resolution and so the criteria are relaxed. For
>example, if a strict criterion from the paper is 2.8 Angstroms
>cutoff, then with 0.4 relaxation the cutoff becomes 3.2 Angstroms.
>We set the default relaxation amounts to what we felt gives
>reasonable results on most PDB structures. However, we made them
>user-adjustable so that if you don't like them, you can change the
>values to whatever you want.
>I hope this helps,
>Elaine C. Meng, Ph.D.
>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>Department of Pharmaceutical Chemistry
>University of California, San Francisco
>On Sep 22, 2009, at 4:18 AM, 吴雪 wrote:
>> Dear colleague:
>> I have a question about the "find hydrongen bond" in Chimera.
>> The dumb relax constraints in Chimera are "0.04 nm" and "20 degree".
>> I don't understand the meaning of the parameter. 20 degree may
>> means the angle bias the line,but I can't figure out what is the
>> The cutoff of the hydrogen is 0.4nm, and the angle is about 90
>> degree or some other parameters depending on the strength of the
>> hydrogen bond.
>> If we set the constraint as 0.02nm or0.03nm , few hydrogen bonds
>> are found. I don't know the criteria. Can you give me some advice
>> so that I can follow your instruction?
>> Sincerly Yours
>> WU Xue
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