Hi all, I have a MD trajectory from GROMACS and I want to visualize it in Chimera using MD Movie tool. My protein move inside the water box. How I cant fix the protein to see the its dynamics in each frame? I have used VMD for this task, using the RMSD trajectory calculator plugin. Here the trajectory is loaded and then press the Align button. The protein coordinates in each frame is superposed on those from the first frame. Whith this the protein stay in a fixed position. It is this possible in Chimera? On the other hand, It is possible load the trajectory just by every N frames? I have a trajectory with 2 000 000 of frames, and I want to load the trajectory every 100 frames. Thanks in advance Yasser -- Yasser Almeida Hernández, MSc. Center of Molecular Immunology (CIM) System Biology Department 216 St. & 15th Ave, Siboney, Playa P.O.Box 16040, Havana 11600 CUBA Phone: (+53-7) 214-3127 almeida@cim.sld.cu --------------------------------------------------- [http://5.cim.co.cu/cim.gif]
Hi Yasser, (1) Yes, you can specify atoms to be held steady as possible in the view. After loading your trajectory, you can select some atoms (for example, command "select protein" for all protein atoms or "select @CA" for all alpha-carbons) and then choose from the MD Movie menu: Actions... Hold Selection Steady. Then you can un-select the atoms and play the trajectory. It will remember which atoms you had selected when you chose that menu item, and try to keep those from moving around. See the MD Movie manpage: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#moviemenu> (2) You can load the trajectory partly by specifying starting and ending frame, but I don't know of any way to load only every Nth frame. You can play back only every Nth frame, but that's after every one in the specified start-end range is loaded. As far as I know, if somebody wants to only load every Nth frame, they would have to use some other processing program or script to create a new trajectory that only contains those frames. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.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 Mar 7, 2014, at 2:17 PM, Yasser Almeida Hernández wrote:
Hi all, I have a MD trajectory from GROMACS and I want to visualize it in Chimera using MD Movie tool.
My protein move inside the water box. How I cant fix the protein to see the its dynamics in each frame?
I have used VMD for this task, using the RMSD trajectory calculator plugin. Here the trajectory is loaded and then press the Align button. The protein coordinates in each frame is superposed on those from the first frame. Whith this the protein stay in a fixed position.
It is this possible in Chimera?
On the other hand, It is possible load the trajectory just by every N frames? I have a trajectory with 2 000 000 of frames, and I want to load the trajectory every 100 frames.
Thanks in advance Yasser
On Mar 7, 2014, at 2:46 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
(2) You can load the trajectory partly by specifying starting and ending frame, but I don't know of any way to load only every Nth frame. You can play back only every Nth frame, but that's after every one in the specified start-end range is loaded. As far as I know, if somebody wants to only load every Nth frame, they would have to use some other processing program or script to create a new trajectory that only contains those frames. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html>
For some formats, such as Amber, specifying a "step size" greater than 1 will skip reading intervening frames. This isn't the case for Gromacs since Chimera uses the Gromacs "XTC Library" (XTC Library - Gromacs) to read the trajectory coordinates and that library has no facility for skipping any frames. In fact, it will read the entire trajectory regardless of your setting for start/end frames, though only the frames in the start/end range will get translated from the raw floating-point numbers that the XTC Library returns into the atomic coordinate data used by Chimera. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Thanks, I fixed it up the second point with some GROMACS commands. Regards On 07/03/14 17:46, Elaine Meng wrote:
Hi Yasser, (1) Yes, you can specify atoms to be held steady as possible in the view. After loading your trajectory, you can select some atoms (for example, command "select protein" for all protein atoms or "select @CA" for all alpha-carbons) and then choose from the MD Movie menu: Actions... Hold Selection Steady. Then you can un-select the atoms and play the trajectory. It will remember which atoms you had selected when you chose that menu item, and try to keep those from moving around. See the MD Movie manpage: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#moviemenu>
(2) You can load the trajectory partly by specifying starting and ending frame, but I don't know of any way to load only every Nth frame. You can play back only every Nth frame, but that's after every one in the specified start-end range is loaded. As far as I know, if somebody wants to only load every Nth frame, they would have to use some other processing program or script to create a new trajectory that only contains those frames. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.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 Mar 7, 2014, at 2:17 PM, Yasser Almeida Hernández wrote:
Hi all, I have a MD trajectory from GROMACS and I want to visualize it in Chimera using MD Movie tool.
My protein move inside the water box. How I cant fix the protein to see the its dynamics in each frame?
I have used VMD for this task, using the RMSD trajectory calculator plugin. Here the trajectory is loaded and then press the Align button. The protein coordinates in each frame is superposed on those from the first frame. Whith this the protein stay in a fixed position.
It is this possible in Chimera?
On the other hand, It is possible load the trajectory just by every N frames? I have a trajectory with 2 000 000 of frames, and I want to load the trajectory every 100 frames.
Thanks in advance Yasser .
-- Yasser Almeida Hernández, MSc. Center of Molecular Immunology (CIM) System Biology Department 216 St. & 15th Ave, Siboney, Playa P.O.Box 16040, Havana 11600 CUBA Phone: (+53-7) 214-3127 almeida@cim.sld.cu --------------------------------------------------- [http://5.cim.co.cu/cim.gif]
participants (3)
-
Elaine Meng -
Eric Pettersen -
Yasser Almeida Hernández