VMD-L Mailing List

From: Yarrow Madrona (amadrona_at_uci.edu)
Date: Sun Apr 07 2013 - 13:27:04 CDT

Wow,
That was too easy. Sorry about the dumb question. I am a VMD begginer.
>
> W dniu 07.04.2013 03:46, Yarrow Madrona pisze:
>> Hello,
>>
>> Does anyone know how to visualize water movement over the course of a
>> trajectory?
>>
>> I know how to select waters within a distance for a given frame. However
>> since they are entering and leaving the index numbers will change.
> Select "water and same residue as within 5 of name FE" as the OP
> suggested, then go to the "Trajectory" tab of the Graphical
> Representations window and check "Update Selection Every Frame".
> Pawel
>> I can
>> write out all of the PDBs and read them back in but I am wondering if
>> there is some script out there that will follow only waters that show up
>> within a distance of the active site regardless of the index number.
>>
>> For example water "1" leaves and 20 frames later water "200" enters
>> within
>> 5 angstroms of a FE atom. I want to be able to visualize the water 1
>> while
>> it is within 5 angstroms and the water 200 while it is within 5
>> angstroms
>> but not when they are greater than 5 angstroms. Thank you for any help
>> you
>> can provide.
>>
>>
>>
>>
>
> 

-- 
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697