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> 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> 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> on behalf of Pius >> Padayatti <ppadaya...@gmail.com> >> *Sent:* Tuesday, August 15, 2023 8:24 PM >> *To:* CCP4BB@JISCMAIL.AC.UK <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$> >> *Pius Padayatti* >> >> >> >> >> On Tue, Aug 15, 2023 at 5:20 PM khaja faisal tarique < >> khajafaisaltari...@gmail.com> wrote: >> >> Hi everyone >> >> Is there any way to make surface representation of a protein structure >> similar to the 'Illustrate: Non-photorealistic Biomolecular >> Illustration' (https://ccsb.scripps.edu/illustrate/ >> <https://urldefense.com/v3/__https://ccsb.scripps.edu/illustrate/__;!!GNU8KkXDZlD12Q!9eD_ProG0wUZ-JErjGALFQIrpgJlQO_bYGkQ0_iklgY0qfFv6IblDBIQ_JwWVq4rFViNFwN_v8t_mnr6vekgjdM7$>) >> using scripts in Pymol ? It will be really helpful if someone can share >> this with me. >> >> Thanks >> >> Faisal >> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!GNU8KkXDZlD12Q!9eD_ProG0wUZ-JErjGALFQIrpgJlQO_bYGkQ0_iklgY0qfFv6IblDBIQ_JwWVq4rFViNFwN_v8t_mnr6vZS2nRni$> >> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!GNU8KkXDZlD12Q!9eD_ProG0wUZ-JErjGALFQIrpgJlQO_bYGkQ0_iklgY0qfFv6IblDBIQ_JwWVq4rFViNFwN_v8t_mnr6vZS2nRni$> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
