Hi Brenton
The script seems to work for me
A couple of questions:
-
Why aren’t you installing PyMOL from the repository?
sudo apt-get install pymol
-
Are you sure that the name of the pdb file is correct? (remember that
names are case sensitive)
Cheers,
Osvaldo
On Fri, Jun 5, 2015 at 12:05 AM, Brenton Horne <brentonhorn...@gmail.com>
wrote:
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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