[Chimera-users] question about Chimera

吴雪 wuxue at nankai.edu.cn
Tue Sep 22 17:18:10 PDT 2009

Dear Elaine:
    Thank you very much for your instruction.
   We'll follow your guide.
    Best wishes
    WU Xue

>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  
>> 0.04nm.
>> 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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