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:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Carter, Charlie Gesendet: Dienstag, 6. Mai 2014 19:16 An: CCP4BB@JISCMAIL.AC.UK 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
