Many thanks to Tim and Nat for, respectively, answering both questions fully,
and to Ethan Merritt for subsequent help!!
Charlie
On May 6, 2014, at 1:24 PM, Tim Gruene wrote:
> 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
>
> GPG Key ID = A46BEE1A
>
