Hi Faisal, You can make similar striking images with the illustrative1 and 2 options in Qutemol https://sourceforge.net/projects/qutemol/. Qutemol ran on Windows10 for me this morning. It does not run on the newer macOS operating systems. Only the binaries are available. It has not been updated since 2007.
Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function COBRE in Structural Biology: https://www.ou.edu/structuralbiology ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of khaja faisal tarique <khajafaisaltari...@gmail.com> Sent: Wednesday, August 16, 2023 6:46 AM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] ILLUSTRATE in PYMOL Thanks all. I am almost there making similar figs as in ILLUSTRATE. It is amazing. Just wondering if we can make similar stuffs in ChimeraX ?. Faisal On Tue, 15 Aug 2023, 23:22 Jared Sampson, <jared.samp...@columbia.edu<mailto:jared.samp...@columbia.edu>> wrote: Hi Faisal - In addition to the `specular`, `ray_trace_mode`, and `ray_trace_gain` settings Blaine pointed out, you can also adjust the `direct` and `ambient` lighting settings, as well as `light_count` (which I believe only affects direct and specular lighting, not ambient). For example, these worked pretty well for me: ``` set ray_trace_mode, 3 set ray_trace_gain, 0 set specular, 0 set direct, 0 set ambient, 0.9 ``` Note that you'll have to ray trace (`ray`) to see the outlines. Also it looks like the tRNA image on the CCSB Illustrate site uses slightly different colors for different parts of the molecule (phosphate, sugar, base), which is a nice effect. Hope that helps. Cheers, Jared On Tue, Aug 15, 2023 at 10:40 PM Mooers, Blaine H.M. (HSC) <blaine-moo...@ouhsc.edu<mailto:blaine-moo...@ouhsc.edu>> wrote: Hi Faisal, I made a number of such figures several years ago. I finally found the code. Load the molecule of interest into PyMOL and paste the following code onto the command line just below the command history window. I was using our school colors: crimson and cream. Ligands are colored crimson. Change to suit your needs. as surface set_color crimsom, [165,42,42]; set_color cream, [221,203,164]; color crimsom, org; color cream, not org; remove solvent set_color bground, [252,250,249]; bg_color bground; # set the view # orient all within 8 of org # set the lights, ray tracing setttings # to get the Goodsell-like rendering unset specular set ray_trace_gain, 0 set ray_trace_mode, 3 bg_color white set ray_trace_color, black set depth_cue, 0 #ray png Goodsell1test.png, 1200,1200,600,1 Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function COBRE in Structural Biology: https://www.ou.edu/structuralbiology ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Pius Padayatti <ppadaya...@gmail.com<mailto:ppadaya...@gmail.com>> Sent: Tuesday, August 15, 2023 8:24 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: [EXTERNAL] Re: [ccp4bb] ILLUSTRATE in PYMOL https://pymolwiki.org/index.php/APBS<https://urldefense.com/v3/__https://pymolwiki.org/index.php/APBS__;!!GNU8KkXDZlD12Q!9eD_ProG0wUZ-JErjGALFQIrpgJlQO_bYGkQ0_iklgY0qfFv6IblDBIQ_JwWVq4rFViNFwN_v8t_mnr6vVLzKnD4$> Pius Padayatti On Tue, Aug 15, 2023 at 5:20 PM khaja faisal tarique <khajafaisaltari...@gmail.com<mailto:khajafaisaltari...@gmail.com>> wrote: Hi everyone Is there any way to make surface representation of a protein structure similar to the 'Illustrate: Non-photorealistic Biomolecular Illustration' (https://ccsb.scripps.edu/illustrate/<https://urldefense.com/v3/__https://ccsb.scripps.edu/illustrate/__;!!GNU8KkXDZlD12Q!9eD_ProG0wUZ-JErjGALFQIrpgJlQO_bYGkQ0_iklgY0qfFv6IblDBIQ_JwWVq4rFViNFwN_v8t_mnr6vekgjdM7$>) using scripts in Pymol ? It will be really helpful if someone can share this with me. 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