[Chimera-users] Chimera-users Digest, Vol 60, Issue 4
Boyle, Joseph J
joseph.boyle at imperial.ac.uk
Thu Apr 3 07:58:37 PDT 2008
Hello,
Is it possible to use Chimera to dock a small ligand into a binding pocket pdb - and if so how is the ligand imported into the protein pdb file ?
Yours Sincerely,
Joseph Boyle
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Sent: Thu 03/04/2008 8:41 AM
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Subject: Chimera-users Digest, Vol 60, Issue 4
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Today's Topics:
1. Re: Smooth Trajectory in MD Movie Tool (Eric Pettersen)
2. Re: Smooth Trajectory in MD Movie Tool (Yan Liang)
3. chimera manual (bala)
----------------------------------------------------------------------
Message: 1
Date: Wed, 2 Apr 2008 16:37:42 -0700
From: Eric Pettersen <pett at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Smooth Trajectory in MD Movie Tool
To: Yan Liang <liangyan at cems.umn.edu>
Cc: Chimera forum <chimera-users at cgl.ucsf.edu>
Message-ID: <7524F1C4-94F1-487C-A67F-FA6A5B4778DB at cgl.ucsf.edu>
Content-Type: text/plain; charset="utf-8"
Hi Yan,
You _could_ write a script to do the averaging, but you would pretty
much have to be an expert on how Chimera handles trajectory data to
be able to write it in any reasonable amount of time. Since I am
such an expert, I've written the script for you and attached it to
this message. To do the averaging, simply have your trajectory open
and then open the script (either with the File...Open menu or with
the "open" command).
Note that the script rewrites the coordinates of the trajectory.
The only way to restore the trajectory to the "unaveraged" state is
by reopening the original files. The main parameter in the script
you might want to change is the "window" variable, which controls how
many adjacent frames contribute to the averaging. The value in the
script right now is 2, which means that the two frames to each side
of a frame contribute to the average (with further-away frames
contributing less).
--Eric
?
On Apr 2, 2008, at 2:36 PM, Yan Liang wrote:
> Thank you very much Eric. I have tried "Hold selection steady"
> function, and it helps a lot to reduce the overall movement of the
> large molecule. But as for the residuals, they are still very shaky.
>
> I am thinking about writing a script to average the movement of
> each atom, but I have no experience in Chimera scripting. Do you
> think it is possible to write such scripts in Chimera? Thanks.
>
> Sincerely,
>
> Yan Liang
> Graduate Student
> Department of Chemical Engineering and Materials Science
> University of Minnesota
>
>
>
> On Apr 2, 2008, at 1:42 PM, Eric Pettersen wrote:
>> Hi Yan,
>> Chimera doesn't yet support smoothing per se. What you can do is
>> use "Hold selection steady" in MD Movie's Actions menu to hold one
>> or more atoms (possibly all atoms) as steady as possible across
>> the trajectory -- which will mostly eliminate the translational
>> component of the "shakiness". This "holding steady" is most
>> useful for small-molecule trajectories and replica-exchange
>> trajectories.
>>
>> --Eric
>>
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>> http://www.cgl.ucsf.edu <http://www.cgl.ucsf.edu/>
>>
>>
>> On Apr 2, 2008, at 10:44 AM, Yan Liang wrote:
>>> Hi
>>>
>>> I am using Chimera to make a MD movie. The problem is the movie
>>> is too
>>> shaky. Is it possible to smooth the trajectory by writing a Per-
>>> Frame
>>> script in MD Movie tool?
>>>
>>> Thanks,
>>>
>>> Yan Liang
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>
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Message: 2
Date: Wed, 2 Apr 2008 21:17:19 -0500
From: Yan Liang <liangyan at cems.umn.edu>
Subject: Re: [Chimera-users] Smooth Trajectory in MD Movie Tool
To: Eric Pettersen <pett at cgl.ucsf.edu>
Cc: Chimera forum <chimera-users at cgl.ucsf.edu>
Message-ID: <D529D4D5-ADEA-4D01-B4C7-5AF51D311251 at cems.umn.edu>
Content-Type: text/plain; charset="us-ascii"
It works great. Thank you so much, Eric.
Sincerely,
Yan Liang
Graduate Student
Department of Chemical Engineering and Materials Science
University of Minnesota
On Apr 2, 2008, at 6:37 PM, Eric Pettersen wrote:
> Hi Yan,
> You _could_ write a script to do the averaging, but you would
> pretty much have to be an expert on how Chimera handles trajectory
> data to be able to write it in any reasonable amount of time. Since
> I am such an expert, I've written the script for you and attached it
> to this message. To do the averaging, simply have your trajectory
> open and then open the script (either with the File...Open menu or
> with the "open" command).
> Note that the script rewrites the coordinates of the trajectory.
> The only way to restore the trajectory to the "unaveraged" state is
> by reopening the original files. The main parameter in the script
> you might want to change is the "window" variable, which controls
> how many adjacent frames contribute to the averaging. The value in
> the script right now is 2, which means that the two frames to each
> side of a frame contribute to the average (with further-away frames
> contributing less).
>
> --Eric
>
> <avg.py>
>
> On Apr 2, 2008, at 2:36 PM, Yan Liang wrote:
>> Thank you very much Eric. I have tried "Hold selection steady"
>> function, and it helps a lot to reduce the overall movement of the
>> large molecule. But as for the residuals, they are still very shaky.
>>
>> I am thinking about writing a script to average the movement of
>> each atom, but I have no experience in Chimera scripting. Do you
>> think it is possible to write such scripts in Chimera? Thanks.
>>
>> Sincerely,
>>
>> Yan Liang
>> Graduate Student
>> Department of Chemical Engineering and Materials Science
>> University of Minnesota
>>
>>
>>
>> On Apr 2, 2008, at 1:42 PM, Eric Pettersen wrote:
>>> Hi Yan,
>>> Chimera doesn't yet support smoothing per se. What you can do is
>>> use "Hold selection steady" in MD Movie's Actions menu to hold one
>>> or more atoms (possibly all atoms) as steady as possible across
>>> the trajectory -- which will mostly eliminate the translational
>>> component of the "shakiness". This "holding steady" is most
>>> useful for small-molecule trajectories and replica-exchange
>>> trajectories.
>>>
>>> --Eric
>>>
>>> Eric Pettersen
>>> UCSF Computer Graphics Lab
>>> http://www.cgl.ucsf.edu <http://www.cgl.ucsf.edu/>
>>>
>>>
>>> On Apr 2, 2008, at 10:44 AM, Yan Liang wrote:
>>>> Hi
>>>>
>>>> I am using Chimera to make a MD movie. The problem is the movie
>>>> is too
>>>> shaky. Is it possible to smooth the trajectory by writing a Per-
>>>> Frame
>>>> script in MD Movie tool?
>>>>
>>>> Thanks,
>>>>
>>>> Yan Liang
>>>> _______________________________________________
>>>> Chimera-users mailing list
>>>> Chimera-users at cgl.ucsf.edu
>>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
>>
>
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------------------------------
Message: 3
Date: Thu, 3 Apr 2008 13:16:05 +0530
From: "bala" <bala at igib.res.in>
Subject: [Chimera-users] chimera manual
To: <chimera-users at cgl.ucsf.edu>
Message-ID: <91F147390CA53D44BFADECB36C489D13026ABD at n1ex>
Content-Type: text/plain; charset="iso-8859-1"
Hello all,
I want to have the pdf version of chimera manual/user guide. I am not finding it anywhere ?. Where can i find it. The only pdf i see is the chimera quick reference guide.
Thanks,
Bala
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