Hi Faisal, Not sure about ChimeraX, but you can do quite amazing things with coot as Lucrezia Catapano has shown to us. Tutorial: https://www.youtube.com/watch?v=tCpCmBTgt6s
Cheers, Helena -- Helena Taberman Beamline Scientist, PhD Beamline P11 (PETRA III) Deutsches Elektronen-Synchrotron DESY Notkestrasse 85 22607 Hamburg Germany Phone: +49 40 8998 5546 Email: helena.taber...@desy.de > On 16. Aug 2023, at 13:46, khaja faisal tarique > <khajafaisaltari...@gmail.com> wrote: > > 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 > <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 > > <https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function> > COBRE in Structural Biology: https://www.ou.edu/structuralbiology > <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. > > 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 > <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 > <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/
