Hi Dan and Thomas, ### Had to send message again due to size restriction, now image can be found a link ###
Perhaps this will do the trick, Show the protein as surface and cartoon then set the surface to almost invisible: set transparency, 0.99 Then set the surface transparency to be angle dependent (done through menu, can't find command for it): Setting > Transparency > Angle-dependent I have rendered an image of what it looks like, can certainly play around with the surface settings to further clean up the image: https://photos.app.goo.gl/7CGZY1Zyrihjw4D96 Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist The University of Sydney School of Pharmacy | Faculty of Medicine and Health 424, Brain and Mind Centre | The University of Sydney | NSW 2050 Email: akus8...@uni.sydney.edu.au https://photos.app.goo.gl/7CGZY1Zyrihjw4D96 On 23/6/20, 5:28 pm, "Thomas Holder" <thomas.hol...@schrodinger.com> wrote: Hi Dan, I think in PyMOL you can only do this in two steps and compose the two images, e.g. with ImageMagick. # white background bg white # step 1 as surface set ray_trace_mode, 2 png surface.png, ray=1 # step 2 hide surface show cartoon set cartoon_cylindrical_helices set ray_trace_mode, 1 png cartoon.png, ray=1 # If you have ImageMagick installed system composite surface.png cartoon.png combined.png load combined.png Cheers, Thomas > On Jun 19, 2020, at 4:04 AM, Daniel P Farrell <da...@uw.edu> wrote: > > Hello, > I'm working with some cryo-EM density and I'm trying to get my isosurface or volume (whichever's easier) to display transparent except for the curves and turns of the density. > similar to this (done in chimeraX) https://protect-au.mimecast.com/s/qAmgCD1vlpTgWg47HWiw6v?domain=imgur.com > > Does anyone know if this is possible? > > thanks > ~Dan > _______________________________________________ > PyMOL-users mailing list > Archives: https://protect-au.mimecast.com/s/KUWLCE8wmrtRzREwHw5Pkx?domain=mail-archive.com > Unsubscribe: https://protect-au.mimecast.com/s/OaZCCGv0oyCjPjvrTpweYH?domain=sourceforge.net -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. _______________________________________________ PyMOL-users mailing list Archives: https://protect-au.mimecast.com/s/KUWLCE8wmrtRzREwHw5Pkx?domain=mail-archive.com Unsubscribe: https://protect-au.mimecast.com/s/OaZCCGv0oyCjPjvrTpweYH?domain=sourceforge.net _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
