ray
command directly in the scripts, as Pymol
would not give me the opportunity to change anything before tracing (and things I trace take loads of time...). So I write a ray
command, but I comment it out, such as in the following example, cytochrome.pml
:
load http://www.rcsb.org/pdb/files/1c6s.pdb hide everything show sticks, (resname HEC) color orange, (resname HEC) show cartoon bg_color white set_view (\ 0.939850032, 0.167392358, 0.297758341,\ 0.336208642, -0.299271941, -0.892972171,\ -0.060366094, 0.939367712, -0.337551534,\ 0.000000000, 0.000000000, -106.161231995,\ 33.668910980, -4.749122620, -24.822664261,\ -9.742469788, 222.064941406, 0.000000000 ) # ray 800,800
So, to easily generate PNG images from such a file, I wrote the following makefile
snippet, that does the job (as demonstrated by the figure on the right, produced by this very snippet ran on the cytochrome.pml
file above):
%.png: %.pml cd $(dir $<); \ ray_trace_args=`grep -o 'ray.*' $(notdir $<)| tail -n1 | egrep -o '([0-9, ]+)' | sed 's/ //g' `; \ pymol -c -d "@$(notdir $<)" -d "cmd.ray($$ray_trace_args)" -g $@
I hope this snippet will prove useful for others. At any rate, it will prove useful for me ! Just for the record, this protein, represented in cartoon
view, is called cytochrome c6 and is one of the proteins implied in the photosynthesis of some organisms.
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