Greetings,
I want to run a vmd script within my bash script. I am using the text only version of VMD for linux for my windows terminal ubuntu subsystem and I would like to generate code within my bash script which automatically renders the files which I would like to use. I have no gui for my linux version of vmd other than cli. Here is a sample of what I want to do:
#!/bin/bash
cd /mnt/c/MS/
mkdir image
cd image
echo "menu files off
menu files on
display resetview
mol addrep 0
display resetview
mol new {/mnt/c/MS/engvector.pdb} type {pdb} first 0 last -1 step 1 waitfor 1
display shadows on
display ambientocclusion on
display projection Orthographic
color Display Background white
menu color off
axes location Off
scale by 1.001000
menu graphics off
menu graphics on
mol color ResType
mol representation Licorice 0.300000 12.000000 12.000000
mol selection all
mol material Opaque
mol modrep 0 0
menu graphics off
menu vmdmovie on
display fps off
display rendermode Normal
animate goto 0
render snapshot /mnt/c/MS/image/untitled.00000.bmp
exit" > temp_VMD.tcl
vmd -e temp_VMD.tcl
However my bmp image is blank. I'm used to using everything from cli so that I can port it to scripts to decrease prep and increase the amnt of time I have to review results.
Thank you for your time,
Brendan Booth
Steps work fine on windows VMD, it looks like its related to the console. Is there a way to run VMD like I do for grace bat where I just open the program with
-nosafe -hardcopy without ever actually opening a gui? I thought that was what the text version of VMD for linux was..
Hey,
I think the -dispdev option is what you are looking for.
Try to execute like
" vmd -dispdev -e temp_VMD.tcl"
Cheers
Hrm, yeah dispdev doesn't seem to make a difference. I think it is related to the fact that WSL2 linux subsystem on windows does not have a virtual mount for a display in the first place. For grace I am able to avoid the display issue entirely with the hardcopy option but I am thinking that VMD text is still reliant on the display rendering images (hence the render command) as opposed to grace which prints to a file. I'm making this harder than it needs to be as of right now though I'll just use the windows version.
Hey Brendan,
I have tried it on a virtual Ubuntu machine and it's working. If you force it with text mode, vmd cannot render the display and therefore cannot create a bmp figure.
Cheers,
Ali
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