Hi Edel, First make sure you have a recent version of Chimera, like 1.13.1. Older versions do not have the “zeropad” keyword. Also, before trying the perframe stuff you would figure out for yourself what command is right to play back your trajectory. E.g. you’d see if the following command plays it back like you expect. coordset #2 1,31 If not, something is wrong, like your trajectory model is a different number, or it’s not a trajectory model. You have to use trial and error yourself rather than expect a full solution when I don’t know all the details of what you are doing. If you created folder ~/Desktop/chimera/ before running these commands, I don’t know what the problem is. The error seems to be in creating the alias, but I don’t know why it says “sourcing” in the error message. Is this in a script file? Before making a script file, you should just test commands by directly entering them nto the command line, and see if that works. Also if you make a script file, it has to be plain text, NOT a word document. You could try using “report bug” on error dialog, or menu: Help… Report a Bug, and describe/attach everything needed to reproduce the problem. However, I don’t know if it is a bug or if you are doing something wrong. Best, Elaine
On Jul 16, 2019, at 6:16 AM, Edel Fenix <edel.fenix@gmail.com> wrote:
Hi Elaine, Thank you! The model is #2 and it has 31 frames in this animation so for me it should be the following correct?
alias ^getobj export ~/Desktop/chimera/$1.obj perframe getobj zeropad 3; coordset #2 1,31; wait 31; ~perframe
The problem I have is I get the following error message and it only outputs the 001 file. The folder exist and is written to.
Best regards, Edel
<Screenshot 2019-07-16 at 15.15.21.png>
On Mon, 15 Jul 2019 at 18:07, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Edel, You didn’t say what “without success” meant. However, here is a more specific example.
Say your trajectory is model #0 with 800 frames… commands could be something like:
alias ^getobj export ~/Desktop/test/$1.obj perframe getobj zeropad 3; coordset #0 1,800; wait 800; ~perframe
… which would save 001.obj, 002.obj… 800.obj (and 001.mtl, 002.mtl… 800.mtl) in ~/Desktop/test/
The folder should already exist, that is, you would have to create ~/Desktop/test/ before running those commands.
This is almost the same as the first example in the “perframe” manual page, except that instead of roll (rotate) it plays the trajectory with the coordset command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html>
The link you sent was to the documentation of Chimera 1.5.2, VERY old… I hope you aren’t really using such an old version. Chimera is at 1.13.1 now with many improvements since 1.5, both new features and bugfixes. <http://www.rbvi.ucsf.edu/chimera/download.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 15, 2019, at 5:26 AM, Edel Fenix <edel.fenix@gmail.com> wrote:
Exporting per-frame command and getting one OBJ file for each frame would work but I've tried without success.
In this case I want to export an already complete morph confirmation scene loaded as a separate (and only) model in MD Movie with 31 frames to individual wavefront OBJ files.
From MD movie where the model is assembled I can select per-frame and select define script, I've tried using the examples and rewriting them to the best of my ability without success. I don't want it to do anything except export each frame from the MD movie setup in OBJ format. What should I write?
http://www.cgl.ucsf.edu/chimera/1.5.2/docs/UsersGuide/midas/perframe.html
I appreciate the help, Edel
On Thu, 11 Jul 2019 at 23:04, Tom Goddard <goddard@sonic.net> wrote: You should use the Chimera perframe command to write out an OBJ file for each frame of the trajectory. There is nothing in Chimera that will put all the frames in one 3d graphics scene file.
Tom
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