Re: Dealing with netcdf trajectories
Hello Eric, just one question. When I load a netcdf trajectory using: open ./trajectory_part1.nc structureModel #1 Would it be possible to additionally precise the range of the loaded frames e.g. to load the first 5000 frames or in range of 500 to 5000 etc? I also noticed that the maximal number of frames is 9999, isn't it ? Many thanks in advance ! Enrico Il giorno gio 11 apr 2024 alle ore 19:49 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Happy to help. :-)
—Eric
On Apr 11, 2024, at 12:52 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Thank you very much Eric !!
Il giorno mer 10 apr 2024 alle ore 18:24 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Hi Enrico, Add "replace false" to the open command you use when opening the second set of coordinates and it will append those coordinate to the current ones.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 10, 2024, at 2:34 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
Typically having loaded pdb of the system I use the following command to load the netcdf file, which replaces current pdb with the trajectory: open ./trajectory_part1.nc structureModel #1
would it be possible to load in the same section the second part of the same trajectory and merge the both into the same ensemble ? E.g. if I run subsequently the same command with another trajectory, it will produce another ensemble related to the second trajectory (and not merge the both together): open ./stripped_*part2.nc structureModel #1
Many thanks in advance!
Enrico _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
ah I've just found that it could be actually specified by the start X end Y step Z so my question is just about the maximal number of the frames ? Are there advantages using other formats besides netcf, like trr, dcd, xtc in terms of the performance ? Enrico Il giorno mar 16 apr 2024 alle ore 09:40 Enrico Martinez < jmsstarlight@gmail.com> ha scritto:
Hello Eric,
just one question. When I load a netcdf trajectory using: open ./trajectory_part1.nc structureModel #1
Would it be possible to additionally precise the range of the loaded frames e.g. to load the first 5000 frames or in range of 500 to 5000 etc? I also noticed that the maximal number of frames is 9999, isn't it ?
Many thanks in advance !
Enrico
Il giorno gio 11 apr 2024 alle ore 19:49 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Happy to help. :-)
—Eric
On Apr 11, 2024, at 12:52 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Thank you very much Eric !!
Il giorno mer 10 apr 2024 alle ore 18:24 Eric Pettersen < pett@cgl.ucsf.edu> ha scritto:
Hi Enrico, Add "replace false" to the open command you use when opening the second set of coordinates and it will append those coordinate to the current ones.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 10, 2024, at 2:34 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
Typically having loaded pdb of the system I use the following command to load the netcdf file, which replaces current pdb with the trajectory: open ./trajectory_part1.nc structureModel #1
would it be possible to load in the same section the second part of the same trajectory and merge the both into the same ensemble ? E.g. if I run subsequently the same command with another trajectory, it will produce another ensemble related to the second trajectory (and not merge the both together): open ./stripped_*part2.nc structureModel #1
Many thanks in advance!
Enrico _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Enrico,
On Apr 16, 2024, at 12:48 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
ah I've just found that it could be actually specified by the start X end Y step Z
Glad you found it.
so my question is just about the maximal number of the frames ?
As far as I know there is no limit to the number of trajectory frames. What leads you to believe the limit is 9999?
Are there advantages using other formats besides netcf, like trr, dcd, xtc in terms of the performance ?
I do not know. —Eric
Enrico
Il giorno mar 16 apr 2024 alle ore 09:40 Enrico Martinez <jmsstarlight@gmail.com <mailto:jmsstarlight@gmail.com>> ha scritto:
Hello Eric,
just one question. When I load a netcdf trajectory using: open ./trajectory_part1.nc <http://trajectory_part1.nc/> structureModel #1
Would it be possible to additionally precise the range of the loaded frames e.g. to load the first 5000 frames or in range of 500 to 5000 etc? I also noticed that the maximal number of frames is 9999, isn't it ?
Many thanks in advance !
Enrico
Il giorno gio 11 apr 2024 alle ore 19:49 Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> ha scritto:
Happy to help. :-)
—Eric
On Apr 11, 2024, at 12:52 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Thank you very much Eric !!
Il giorno mer 10 apr 2024 alle ore 18:24 Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> ha scritto:
Hi Enrico, Add "replace false" to the open command you use when opening the second set of coordinates and it will append those coordinate to the current ones.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 10, 2024, at 2:34 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear Chimera-X users !
Typically having loaded pdb of the system I use the following command to load the netcdf file, which replaces current pdb with the trajectory: open ./trajectory_part1.nc <http://trajectory_part1.nc/> structureModel #1
would it be possible to load in the same section the second part of the same trajectory and merge the both into the same ensemble ? E.g. if I run subsequently the same command with another trajectory, it will produce another ensemble related to the second trajectory (and not merge the both together): open ./stripped_*part2.nc <http://part2.nc/> structureModel #1
Many thanks in advance!
Enrico _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
just retested it again on a small system, apparently it works with 10k frames as well .. 😃 Yours with thanks Enrico Il giorno mar 16 apr 2024 alle ore 19:50 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Hi Enrico,
On Apr 16, 2024, at 12:48 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
ah I've just found that it could be actually specified by the start X end Y step Z
Glad you found it.
so my question is just about the maximal number of the frames ?
As far as I know there is no limit to the number of trajectory frames. What leads you to believe the limit is 9999?
Are there advantages using other formats besides netcf, like trr, dcd, xtc in terms of the performance ?
I do not know.
—Eric
Enrico
Il giorno mar 16 apr 2024 alle ore 09:40 Enrico Martinez < jmsstarlight@gmail.com> ha scritto:
Hello Eric,
just one question. When I load a netcdf trajectory using: open ./trajectory_part1.nc structureModel #1
Would it be possible to additionally precise the range of the loaded frames e.g. to load the first 5000 frames or in range of 500 to 5000 etc? I also noticed that the maximal number of frames is 9999, isn't it ?
Many thanks in advance !
Enrico
Il giorno gio 11 apr 2024 alle ore 19:49 Eric Pettersen < pett@cgl.ucsf.edu> ha scritto:
Happy to help. :-)
—Eric
On Apr 11, 2024, at 12:52 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Thank you very much Eric !!
Il giorno mer 10 apr 2024 alle ore 18:24 Eric Pettersen < pett@cgl.ucsf.edu> ha scritto:
Hi Enrico, Add "replace false" to the open command you use when opening the second set of coordinates and it will append those coordinate to the current ones.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 10, 2024, at 2:34 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
Typically having loaded pdb of the system I use the following command to load the netcdf file, which replaces current pdb with the trajectory: open ./trajectory_part1.nc structureModel #1
would it be possible to load in the same section the second part of the same trajectory and merge the both into the same ensemble ? E.g. if I run subsequently the same command with another trajectory, it will produce another ensemble related to the second trajectory (and not merge the both together): open ./stripped_*part2.nc structureModel #1
Many thanks in advance!
Enrico _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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