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) ! Kenward
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@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
...
-- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca