Dear Charlie, I still use molscript quite a bit, it is not so old fashioned as you might think. Raster3D is even in the standard repository of Debian.
You need to use the command line option '-r' in order to create Raster3D
output. You can use the pipe
molscript -r -in your_molscipt.inp | render -png your_file.png
You get all command lines with 'molscript -h' and 'render -h'
respectively, and their html documentation is really good if you need
fine tuning.
Since png is state-of-the-art bitmap format, you can use the program of
your choice for editing. I use gimp, if I need it at all, but sometimes
also edit the Raster3D file manually, e.g. for setting labels.
Coot also creates output for Raster3D and also for Povray, in case this
might be an option for you. That way you can easily include maps in the
rendered file.
Regards,
Tim
On 05/06/2014 07:15 PM, Carter, Charlie wrote:
> I need help with a problem whose dimensions I perceive, but cannot surmount.
>
> It appears to be very important for me to re-make an illustration I made long
> ago using molscript. For various reasons, I cannot think of a way to do this
> with Pymol. I want to highlight active site residues by showing only the
> alpha carbons at approximately their van der Waals radii or a bit bigger.
>
> I resurrected molscript 2.1.2, recompiled it on my iMac and ran the input
> file, creating what appears to be a postscript file. Distiller converts it to
> a pdf file, but the image has all the wrong colors and hasn't been ray
> traced. The original illustration was prepared on a unix workstation that had
> a flow of programs that involved raster3D creating what I think were .png
> files, which I viewed and manipulated with a suite of unix-based public
> domain graphics utilities whose names I cannot recall, but they were much in
> vogue at the time.
>
> The header of the file output by molscript is:
>
> %!PS-Adobe-3.0
> %%BoundingBox: (atend)
> %%Creator: MolScript v2.1.2, Copyright (C) 1997-1998 Per J. Kraulis
> %%For: charleswcarterjr
> %%DocumentNeededResources: font Times-Roman Symbol
> %%Pages: 1
> %%EndComments
> %%BeginProlog
> 50 dict begin
> /R { setrgbcolor } bind def
>
> which suggests it is a .ps file.
>
> Can anyone help me recover the rest of the software train that produced the
> images I once made?
>
> Or alternately how to create a similar view using pymol?
>
> Many thanks,
>
> Charlie
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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