Hi, The ‘set transparency’ command will set the transparency of a surface (e.g. the interface between a protein and the surrounding water). I think the command you’re after is ‘set cartoon_transparency’ (https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels). Depending on your choice of representation, see also ‘set sphere_transparency’ and ‘set stick_transparency’.
Cheers, Paul From: sunyeping via PyMOL-users<mailto:pymol-users@lists.sourceforge.net> Sent: 03 December 2018 03:02 To: pymol-users<mailto:pymol-users@lists.sourceforge.net> Subject: [PyMOL] how to make selected residues blurry? Dear all, Could you please check this figure at the following link? https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0%2Fview%3Fusp%3Dsharing&data=01%7C01%7Cpaul.smith%40kcl.ac.uk%7C2bf336b34d554aedf37e08d658cbb9c8%7C8370cf1416f34c16b83c724071654356%7C0&sdata=tgPlIectw3pV9ppkv9IeX6YsqnRepi%2Bmb75aB0UzGPk%3D&reserved=0> The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are: residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command: set transparency, 0.8, sele but it doesn't work. Could anyone help me figure it out？ With sincere thanks.
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