[Chimera-users] Morphing a residue through MD trajectories

Kenward Vaughan kay_jay at earthlink.net
Sun Aug 2 10:55:09 PDT 2015

On 08/02/2015 10:37 AM, Elaine Meng wrote:
> Hi Ken, I thought George was asking about showing something as
> completely immobile (frozen) at the same time as the movements of
> some of the atoms in his trajectory.  That is what you could do with
> the separate PDB file. However, I could have misinterpreted the
> question.  Sometimes it is hard to guess what is going on!
> There is a “hold steady” option in MD Movie that tries to keep the
> (user-)specified atoms *within* the trajectory in the same place as
> much as possible. In that case, there will generally be slight
> movements as the relationships among even the specified atoms
> changes, but it should cut down on the large-scale movements of that
> group as a whole.  In that case you would not need a separate PDB
> file for anything.
> The option is in the MD Movie menu: Actions… Hold selection steady.

Merci (as usual) !


> Best, 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 Aug 1, 2015, at 8:38 AM, Kenward Vaughan <kay_jay at earthlink.net>
> wrote:
>> On 08/01/2015 07:58 AM, Elaine Meng wrote:
>>> Hi George, You can hide whatever parts of the trajectory
>>> structure you want, just like for other structures in Chimera.
>>> So even if the trajectory includes a protein receptor plus
>>> ligand, you could hide the protein ribbons/atoms and only show
>>> the ligand during playback. For your frozen receptor, you can
>>> have another PDB file opened the regular way (directly in
>>> Chimera, not as a trajectory) at the same time; just keep it
>>> displayed while you are playing back the trajectory. Elaine
>> Hi Elaine, Following up on this myself with a question...  As
>> George was describing things I found myself wondering if what you
>> were suggesting actually accomplishes what *I* was visualizing?
>> (Interesting 3-way conversation here??)
>> Things bounce around during a trajectory.  Can the various steps be
>> auto rotated/oriented/scaled so that the ligand does not appear to
>> move from one frame to another?
>> Is this what is accomplished by having the other file opened?
>> Chau! Kenward

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