Hi Brenton,
regarding "SVN download doesn't color by secondary structure":
If you want to use the SVN version, then please always have a look at the top
of the ChangeLog, or follow SVN commit messages. In the latest commit I changed
the default of the "ignore_case" setting to "off". This mean that you have to
select with upper case ss arguments ("ss H" instead of "ss h"), or set the
ignore_case setting in your script. "ignore_case" is for the lazy coder and was
the default in PyMOL ever since, but it's not practical anymore since it
becomes common to use upper and lower case chain identifiers in big structures.
The setting affects all of the selection language, not just chains.
Cheers,
Thomas
On 04 Jun 2015, at 23:05, 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.
> Thanks for your time,
> Brenton
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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