Hi,
bug 1)
I think the problem is with what is saved in the pse. The pse which is
giving me these problems does not display the message I can't display
an oversized image. So I decided to recreate the scene from my .pml
command file.
bug 2)
Now this leads to another possible bug. I setup my scene with the .pml
file, and do ray 1200,1200 I get the I can't display an oversized
image message. Then I do png file.png while the message is still on the
display window and I get the ray-traced image. But when you open
file.png some of the carbon bonds/atoms in stick mode that should be
gray (as seen in the display window) are green in the file.png (I tried
looking at the image using eog, gimp, konqueror and all show the same
problem).
bug 3)
using movie - render frames no longer shows a rendered frame in the
display window. Is this the normal behavior, because it used to work?
Tried restarted several times and used only the .pml command file and
not the buggy pse, but no luck.
bug 4)
When movie - render frames used to work, I believe it displayed all the
colors properly, but the same thing happens as with bug 2 when you
output the png (some carbon atoms that are gray in the display window
become green in the png file).
Here are the contents of the pml file causing all the bugs:
load file.pdb
hide all
bg_color white
create 901, (resi 901 and chain a)
show sticks, (901)
color gray, (elem c)
color red, (elem o)
color yellow, (elem p,pa,pb,pg)
color cyan, (elem s)
create near901A, (byres (901 around 3 and chain a))
show sticks, (near901A)
color green, (near901A and elem c)
create near901B, (byres (901 around 3 and chain b))
show sticks, (near901B)
color cyan, (near901B and elem c)
set orthoscopic=1
set antialias=1.0
Now here is a very similar .pml file which does not cause all these
bugs, the only difference is that in the buggy pml I use the byres and
around commands while in this one I explicitly identify which residues I
want displayed.
load file.pdb
hide all
bg_color white
create 903, (resi 903 and chain a)
show sticks, (903)
color gray, (elem c)
color red, (elem o)
color yellow, (elem p,pa,pb,pg)
color cyan, (elem s)
create near903A, (resi 218,241,89 and chain a)
show sticks, (near903A)
color green, (near903A and elem c)
create near903B, (resi 230,232 and chain b)
show sticks, (near903B)
color cyan, (near903B and elem c)
set orthoscopic=1
set antialias=1.0
The only explanation I can give for the green carbons being outputted
rather than gray is that the byres around commands are also coloring the
901 carbon atoms green (since it is itself within 3 angstroms), but in
the display window I see it as gray ..strange.
Sorry if this is really confusing, but I hope it's some error in the pml
and not in pymol.
Thanks,
Sabuj Pattanayek
Matt Franklin wrote:
Sabuj Pattanayek wrote:
Hi,
I set smooth lines from the menu, then I did:
set orthoscopic=1
set antialias=1
ray 1200,1200
png file.png
and file.png was the same size as the display window (less than
1200x1200), and I could still see jagged lines, as if it outputted
exactly the quality seen in the display window. I got this to work
once with a different pse file, tried restarting pymol but I can't get
it to work anymore. I'm using 0_98beta27 on linux.
Thanks,
Sabuj Pattanayek
This could be a genuine bug, but did you do anything between the ray
command and the png command? If you click in the graphics window, the
raytraced image goes away and you get the OpenGL image again. Was the
message I can't display an oversized image still in the window when
you did the png command?
- Matt
