Hi,
I installed PyMOL on 32 bit Ubuntu 15.04 by following the Linux install
guide on PyMOL Wiki. Although I ended up redoing it using the tarball
available at Source Forge instead of the directory downloaded via
Subversion (SVN) as SVN downloads an unstable release 1.7.7.1 which I
found was unresponsive to colouring commands for secondary structures
displayed in cartoon mode:
color red, ss s
color yellow, ss h
color blue, ss l+""
Here’s the code I used to install the tarball:
cd /tmp
wget -c
http://internode.dl.sourceforge.net/project/pymol/pymol/1.7/pymol-v1.7.6.0.tar.bz2
tar -xvf pymol-v1.7.6.0.tar.bz2
rm /tmp/pymol-v1.7.6.0.tar.bz2
sudo chmod 777 -R pymol
cd pymol
# Configuration and installation
prefix=/opt/pymol-svn
modules=$prefix/modules
# enable c++11
export CPPFLAGS="-std=c++0x"
sudo python setup.py build install \
--home=$prefix \
--install-lib=$modules \
--install-scripts=$prefix
sudo chmod 777 -R /tmp/pymol
python setup.py build install \
--home=$prefix \
--install-lib=$modules \
--install-scripts=$prefix
sudo python setup.py build install \
--home=$prefix \
--install-lib=$modules \
--install-scripts=$prefix
you may wish to know why I repeated the python setup.py build install
line three times. Well I find that if I use just one it jams in the
layer1 directory (which I believe to be the result of the /build
subdirectory of /tmp/pymol having writes permission issues, which is why
I added the chmod line after it). For whatever reason doing one more
build install line with sudo in front doesn’t suffice and gives errors,
so I do it without the sudo and then do the sudo command afterwards
because otherwise it gives permission errors as it can’t write to
/opt/pymol-svn without root permissions. This bash script successfully
installs PyMOL, but for whatever reason rendering ball and stick models
using POV-Ray doesn't seem to work, although I can render cartoon models
using POV-Ray without a problem. I can save the ball and stick models in
PNG format via the GUI without a problem though. This is the script I'm
using to create the ball-and-stick models I'm attempting to render with
POV-Ray:
delete all
load 2hyy.pdb1
hide everything
h_add r. STI
show sticks, r. STI
show spheres, r. STI
set stick_radius, .07
set sphere_scale, .18
set sphere_scale, .13, elem H
set bg_rgb=[1, 1, 1]
set stick_quality, 50
set sphere_quality, 4
color black, elem C and organic
color red, elem O and organic
color slate, elem N and organic
color white, elem H and organic
set stick_color, black
set ray_trace_mode, 1
set ray_texture, 2
set antialias, 3
set ambient, 0.5
set spec_count, 5
set shininess, 50
set specular, 1
set reflect, .1
set dash_gap, 0
set dash_color, black
set dash_gap, .15
set dash_length, .05
set dash_round_ends, 0
set dash_radius, .05
set valence, 2
set valence_size, 0.2
python
preset.ball_and_stick("r. STI")
python end
orient r. STI
and this is the PML script I use to render the model using POV-Ray:
set ray_opaque_background, 0
png 2HYY_img0001.png, dpi=500, ray=1, width = 4000, height = 2325
This gives a blank transparent PNG output, namely this
<http://i.imgur.com/FYsDSCl.png>.
Thanks for your time,
Brenton
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