[Chimera-users] Question related to chimera H-bond constraints

[snoze pa]

Thanks Elaine for your reply. In a quick question, I am trying to load
two dcd files in chimera. Both files are obtained from same
simulation(1-50ps first one and 50 to 100ps second one). How can I add
these two dcd files in chimera.. When I am using MD movie tool then it
is showing two window, one for first part and other for second part.
Is it possible to merge both dcd files in chimera. VMD can read
multiple dcd files but I want to use chimera for clear H bond
analysis.
Thank you

On Wed, Mar 24, 2010 at 12:53 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Dear S,
> In both #1 and #2 you have checked "Relax" so you are using the relaxed
> values, and will get the same total (76).  The only difference is coloring:
> in #1 all 76 are colored cyan, whereas in #2 the ones meeting the strict
> criteria (50) are cyan and the ones that do not meet the strict criteria but
> do meet the relaxed criteria (26) are red.  In #3 you only have the strict
> ones.
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Mar 24, 2010, at 10:21 AM, snoze pa wrote:
>
>> Dear Chimera Users,
>>
>> I have a question related to number of hydrogen bonds.
>>
>> 1.  When I am using the Relax H-bond constraints then chimera is
>> showing 76 H-bonds as shown below figure (h bonds are shown in cyan
>> color)
>>
>> http://img260.imageshack.us/img260/6467/screenshotau.png
>>
>> 2. If I will select the option color H bonds not meeting precise
>> criteria differently, then still it shows 76 H bonds with some bonds
>> that do not meet the criteria in red color
>>
>> http://img690.imageshack.us/img690/5607/screenshot1ks.png
>>
>> In 2, Why the red H bonds are different from 1 though H bonds are
>> relaxed. If it is true then why chimera is showing these bonds in
>> Relax H-bond constraints in 1.
>>
>> 3. However, if I will not choose the option to relax H bonds
>> constraints then it is showing 50 H bonds as shown below
>>
>> http://img153.imageshack.us/img153/3822/screenshot2kr.png
>>
>> Thank you very much for your time and help.
>>
>> S
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>
>