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
> 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, <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)
> 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 <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Pius Padayatti
> mailto:ppadaya...@gmail.com>>
> Sent: Tuesday, August 15, 2023 8:24 PM
> To: CCP4BB@JISCMAIL.AC.UK <mailto: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
> 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-JE
