[chimerax-users] saving multiple .obj files from a morph

[Brett Murrah]

I this is working!!!  Thank you.  

Sent from my iPhone

> On Jun 9, 2021, at 11:33 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Minor update:  further tests suggest that the all-on-one line approach will work if a space is inserted between the second quotation mark and the first semicolon.
> 
> Elaine
> 
>> On Jun 9, 2021, at 8:02 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> 
>>> On Jun 9, 2021, at 3:38 AM, Brett Murrah <murrahx5 at att.net> wrote:
>>> 
>>> I’m trying my best to use the perframe command to save each frame / model out from a morph and slider animation after morphing some pdbs.  It is exporting something.. but only 1k files.  I’m not sure what I’m doing wrong.  Any help?   My command is this:
>>> 
>>> perframe "save D:/Projects/OBJs/model$1.obj model #3.$1" frames 10
>>> 
>>> PS, I put model #3 because the ID’s for 1 and 2 are the models I used for the morphs.  The final morph is #3.   If I export each slider frame by hand.. that seems to work.  Trying to automate it best I can.
>>> 
>>> Thanks you for any help!
>>> Brett
>> 
>> 
>> Hi Brett,
>> I'm guessing you meant to send this to chimerax-users at cgl.ucsf.edu (CC'd here, the recommended address for questions). 
>> 
>> The morph #3 is a trajectory model. It does not have the frames as submodels #3.1, 3.2, ... so your save command doesn't make sense.  I don't know what you mean by "1k files" either... do you mean it makes 10 files but they are too small?
>> 
>> You would use "perframe" in combination with "coordset" to replay the existing morph trajectory. E.g. put something like this into a command file (plain text named something.cxc) and then open it in ChimeraX:
>> 
>> perframe "save D:/Projects/OBJs/model$1.obj models #3"
>> coordset #3 1,10; wait 10
>> ~perframe
>> 
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html>
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html>
>> 
>> The reason I say to put it in a command file is to make the commands execute instantly one afer the other.  I expected it to work when I entered them all as one long line in the command line (with semicolon separators) but then I got a parsing error, possibly due to a bug.  E.g. I tried entering this as one long line (the mail tool may choose to break it up):
>> 
>> perframe "save D:/Projects/OBJs/model$1.obj models #3"; coordset #3 1,10; wait 10; ~perframe
>> 
>> ... but that gave an "incomplete quoted text" error which I will report as a bug.
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>> 
>> 
>> 
>