Morphing a residue through MD trajectories
Hi, I have an MD trajectory which I can load successfully on Chimera. My objective is to monitor changes in conformations of one particular residue in the receptor (:123) throughout the trajectory and generate a movie. If I could do this in tandem with a bound ligand so much the better. I’ve tried to follow the instructions but obviously, I get it wrong. I opened the Morph Conformations tool, I selected the trajectory and clicked on Add. This generated a 2nd MD Movie panel of just one frame. Any help would be most welcome Regards George
Hi George, I’m not sure exactly what you are trying to do, but I’m pretty sure there is no reason to use Morph Conformations. As you have seen, that tool creates a new trajectory, it does not use a trajectory as input. Maybe you want to play back this trajectory as a time series. In that case you need to open it in the MD Movie tool (the trajectory viewer). If you have just opened your trajectory PDB file(s) directly in Chimera, it is not treated as a trajectory. First start Chimera with nothing open, then start MD Movie (in menu under Tools… MD/Ensemble Analysis). A dialog will appear requesting the input trajectory file(s). You should change to the proper format setting and then browse to your file location in that dialog. Then your trajectory will be open as a trajectory. You can control the display just like you do with other structures in Chimera, for example showing ligand and other atoms of interest. With MD Movie, besides playback, you can also plot values such as distances and angles, create a movie file, etc. MD Movie documentation: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h...> See also the Trajectory and Ensemble Analysis tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html> I hope this helps, 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 7:25 AM, George Tzotzos <gtzotzos@me.com> wrote:
Hi, I have an MD trajectory which I can load successfully on Chimera. My objective is to monitor changes in conformations of one particular residue in the receptor (:123) throughout the trajectory and generate a movie. If I could do this in tandem with a bound ligand so much the better. I’ve tried to follow the instructions but obviously, I get it wrong. I opened the Morph Conformations tool, I selected the trajectory and clicked on Add. This generated a 2nd MD Movie panel of just one frame. Any help would be most welcome Regards George
Thank you Elaine, I was wondering if I could keep the receptor “frozen” and generate a movie of the conformations of the particular residue of interest. Have a good day George
On 1 Aug 2015, at 17:46, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, I’m not sure exactly what you are trying to do, but I’m pretty sure there is no reason to use Morph Conformations. As you have seen, that tool creates a new trajectory, it does not use a trajectory as input.
Maybe you want to play back this trajectory as a time series. In that case you need to open it in the MD Movie tool (the trajectory viewer). If you have just opened your trajectory PDB file(s) directly in Chimera, it is not treated as a trajectory. First start Chimera with nothing open, then start MD Movie (in menu under Tools… MD/Ensemble Analysis). A dialog will appear requesting the input trajectory file(s). You should change to the proper format setting and then browse to your file location in that dialog. Then your trajectory will be open as a trajectory.
You can control the display just like you do with other structures in Chimera, for example showing ligand and other atoms of interest. With MD Movie, besides playback, you can also plot values such as distances and angles, create a movie file, etc.
MD Movie documentation: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h...>
See also the Trajectory and Ensemble Analysis tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html>
I hope this helps, 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 7:25 AM, George Tzotzos <gtzotzos@me.com> wrote:
Hi, I have an MD trajectory which I can load successfully on Chimera. My objective is to monitor changes in conformations of one particular residue in the receptor (:123) throughout the trajectory and generate a movie. If I could do this in tandem with a bound ligand so much the better. I’ve tried to follow the instructions but obviously, I get it wrong. I opened the Morph Conformations tool, I selected the trajectory and clicked on Add. This generated a 2nd MD Movie panel of just one frame. Any help would be most welcome Regards George
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 On Aug 1, 2015, at 7:52 AM, George Tzotzos <gtzotzos@me.com> wrote:
Thank you Elaine, I was wondering if I could keep the receptor “frozen” and generate a movie of the conformations of the particular residue of interest. Have a good day George
On 1 Aug 2015, at 17:46, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, I’m not sure exactly what you are trying to do, but I’m pretty sure there is no reason to use Morph Conformations. As you have seen, that tool creates a new trajectory, it does not use a trajectory as input.
Maybe you want to play back this trajectory as a time series. In that case you need to open it in the MD Movie tool (the trajectory viewer). If you have just opened your trajectory PDB file(s) directly in Chimera, it is not treated as a trajectory. First start Chimera with nothing open, then start MD Movie (in menu under Tools… MD/Ensemble Analysis). A dialog will appear requesting the input trajectory file(s). You should change to the proper format setting and then browse to your file location in that dialog. Then your trajectory will be open as a trajectory.
You can control the display just like you do with other structures in Chimera, for example showing ligand and other atoms of interest. With MD Movie, besides playback, you can also plot values such as distances and angles, create a movie file, etc.
MD Movie documentation: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h...>
See also the Trajectory and Ensemble Analysis tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html>
I hope this helps, 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 7:25 AM, George Tzotzos <gtzotzos@me.com> wrote:
Hi, I have an MD trajectory which I can load successfully on Chimera. My objective is to monitor changes in conformations of one particular residue in the receptor (:123) throughout the trajectory and generate a movie. If I could do this in tandem with a bound ligand so much the better. I’ve tried to follow the instructions but obviously, I get it wrong. I opened the Morph Conformations tool, I selected the trajectory and clicked on Add. This generated a 2nd MD Movie panel of just one frame. Any help would be most welcome Regards George
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you Elaine. Most helpful as usual George
On 1 Aug 2015, at 17:58, Elaine Meng <meng@cgl.ucsf.edu> 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
On Aug 1, 2015, at 7:52 AM, George Tzotzos <gtzotzos@me.com> wrote:
Thank you Elaine, I was wondering if I could keep the receptor “frozen” and generate a movie of the conformations of the particular residue of interest. Have a good day George
On 1 Aug 2015, at 17:46, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, I’m not sure exactly what you are trying to do, but I’m pretty sure there is no reason to use Morph Conformations. As you have seen, that tool creates a new trajectory, it does not use a trajectory as input.
Maybe you want to play back this trajectory as a time series. In that case you need to open it in the MD Movie tool (the trajectory viewer). If you have just opened your trajectory PDB file(s) directly in Chimera, it is not treated as a trajectory. First start Chimera with nothing open, then start MD Movie (in menu under Tools… MD/Ensemble Analysis). A dialog will appear requesting the input trajectory file(s). You should change to the proper format setting and then browse to your file location in that dialog. Then your trajectory will be open as a trajectory.
You can control the display just like you do with other structures in Chimera, for example showing ligand and other atoms of interest. With MD Movie, besides playback, you can also plot values such as distances and angles, create a movie file, etc.
MD Movie documentation: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h...>
See also the Trajectory and Ensemble Analysis tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html>
I hope this helps, 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 7:25 AM, George Tzotzos <gtzotzos@me.com> wrote:
Hi, I have an MD trajectory which I can load successfully on Chimera. My objective is to monitor changes in conformations of one particular residue in the receptor (:123) throughout the trajectory and generate a movie. If I could do this in tandem with a bound ligand so much the better. I’ve tried to follow the instructions but obviously, I get it wrong. I opened the Morph Conformations tool, I selected the trajectory and clicked on Add. This generated a 2nd MD Movie panel of just one frame. Any help would be most welcome Regards George
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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
On Aug 1, 2015, at 7:52 AM, George Tzotzos <gtzotzos@me.com> wrote:
Thank you Elaine, I was wondering if I could keep the receptor “frozen” and generate a movie of the conformations of the particular residue of interest. Have a good day George
On 1 Aug 2015, at 17:46, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, I’m not sure exactly what you are trying to do, but I’m pretty sure there is no reason to use Morph Conformations. As you have seen, that tool creates a new trajectory, it does not use a trajectory as input.
Maybe you want to play back this trajectory as a time series. In that case you need to open it in the MD Movie tool (the trajectory viewer). If you have just opened your trajectory PDB file(s) directly in Chimera, it is not treated as a trajectory. First start Chimera with nothing open, then start MD Movie (in menu under Tools… MD/Ensemble Analysis). A dialog will appear requesting the input trajectory file(s). You should change to the proper format setting and then browse to your file location in that dialog. Then your trajectory will be open as a trajectory.
You can control the display just like you do with other structures in Chimera, for example showing ligand and other atoms of interest. With MD Movie, besides playback, you can also plot values such as distances and angles, create a movie file, etc.
MD Movie documentation: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h...>
See also the Trajectory and Ensemble Analysis tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html>
I hope this helps,
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 7:25 AM, George Tzotzos <gtzotzos@me.com> wrote:
Hi, I have an MD trajectory which I can load successfully on Chimera. My objective is to monitor changes in conformations of one particular residue in the receptor (:123) throughout the trajectory and generate a movie. If I could do this in tandem with a bound ligand so much the better. I’ve tried to follow the instructions but obviously, I get it wrong. I opened the Morph Conformations tool, I selected the trajectory and clicked on Add. This generated a 2nd MD Movie panel of just one frame. Any help would be most welcome Regards George
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- 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
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. 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
On Aug 1, 2015, at 7:52 AM, George Tzotzos <gtzotzos@me.com> wrote:
Thank you Elaine, I was wondering if I could keep the receptor “frozen” and generate a movie of the conformations of the particular residue of interest. Have a good day George
On 1 Aug 2015, at 17:46, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, I’m not sure exactly what you are trying to do, but I’m pretty sure there is no reason to use Morph Conformations. As you have seen, that tool creates a new trajectory, it does not use a trajectory as input.
Maybe you want to play back this trajectory as a time series. In that case you need to open it in the MD Movie tool (the trajectory viewer). If you have just opened your trajectory PDB file(s) directly in Chimera, it is not treated as a trajectory. First start Chimera with nothing open, then start MD Movie (in menu under Tools… MD/Ensemble Analysis). A dialog will appear requesting the input trajectory file(s). You should change to the proper format setting and then browse to your file location in that dialog. Then your trajectory will be open as a trajectory.
You can control the display just like you do with other structures in Chimera, for example showing ligand and other atoms of interest. With MD Movie, besides playback, you can also plot values such as distances and angles, create a movie file, etc.
MD Movie documentation: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h...>
See also the Trajectory and Ensemble Analysis tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html>
I hope this helps,
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 7:25 AM, George Tzotzos <gtzotzos@me.com> wrote:
Hi, I have an MD trajectory which I can load successfully on Chimera. My objective is to monitor changes in conformations of one particular residue in the receptor (:123) throughout the trajectory and generate a movie. If I could do this in tandem with a bound ligand so much the better. I’ve tried to follow the instructions but obviously, I get it wrong. I opened the Morph Conformations tool, I selected the trajectory and clicked on Add. This generated a 2nd MD Movie panel of just one frame. Any help would be most welcome Regards George
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- 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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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
participants (3)
-
Elaine Meng -
George Tzotzos -
Kenward Vaughan