It can be done with pymol:
In the box in the lower left corner is an item "selecting residues". By clicking on "residues" you can change it to "atoms" or "C-alphas"
When you now click on the appropriate active site atoms, you can select the alpha carbons and a "(sele)" item appears.
In the "(sele)" item you select "sphere" to get your spheres.
The radius of the spheres can be changed in "Setting" (pull-down menu at the top), "Edit All" and "sphere_scale".
However, you may not get the nostalgic retro-look you might be after that way.
Herman
-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Carter, Charlie
Gesendet: Dienstag, 6. Mai 2014 19:16
An: [log in to unmask]
Betreff: [ccp4bb] SOS from last century!
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
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