Re: [ccp4bb] ILLUSTRATE in PYMOL

[khaja faisal tarique]

Thanks everyone for their valuable feedback. It helped a lot.

Best

Faisal

On Tue, 15 Aug 2023, 19:19 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/) using scripts in Pymol ? It will
> be really helpful if someone can share this with me.
>
> Thanks
>
> Faisal
>
>



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] ILLUSTRATE in PYMOL

[khaja faisal tarique]

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, 
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  on behalf of Pius
>> Padayatti 
>> *Sent:* Tuesday, August 15, 2023 8:24 PM
>> *To:* 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=1
>> <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!GNU8KkXDZlD12Q!9eD_ProG0wUZ-JErjGALFQIrpgJlQO_bYGkQ0_iklgY0qfFv6IblDBIQ_JwWVq4rFViNFwN_v8t_mnr6vZS2nRni$>
>>
>>
>> --

[ccp4bb] ILLUSTRATE in PYMOL

[khaja faisal tarique]

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/) using scripts in Pymol ? It will be
really helpful if someone can share this with me.

Thanks

Faisal



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Re: [ccp4bb] saving coordinates with respect to map in ChimeraX

[khaja faisal tarique]

Hi Tristan

I have posted my question in ChimeraX mailing list as well and waiting for
their reply.

What you are suggesting is for Chimera. I dont see any such option in
ChimeraX. That save relative to section does not appear here or may be
there is a different way of saving model relative to map in ChimeraX.

Please correct me if I am wrong.

Faisal

On Mon, 28 Jun 2021, 2:44 pm Tristan Croll,  wrote:

> Hi Faisal,
>
> This is really a question for the ChimeraX-users list (
> chimerax-us...@cgl.ucsf.edu). But the quick run-down: using the File/Save
> dialogue, you'll see a checkbox with "Save relative to model: " and then a
> drop-down menu. Just choose the map in the drop-down menu, and you should
> get the result you want.
>
> Best regards,
> Tristan
> --
> *From:* CCP4 bulletin board  on behalf of khaja
> faisal tarique 
> *Sent:* 28 June 2021 09:43
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* [ccp4bb] saving coordinates with respect to map in ChimeraX
>
> Hello everyone
>
> While doing rigid body fit we know that after placing the coordinate to
> its correct position we can save it with respect to the map. Does anyone
> know if a similar feature exists in ChimeraX ?  Is there a way where the
> coordinates .pdb/cif file can be saved with respect to its map in ChimeraX ?
>
> Thank you
>
> --
> Faisal Tarique Khaja
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] saving coordinates with respect to map in ChimeraX

[khaja faisal tarique]

Hello everyone

While doing rigid body fit we know that after placing the coordinate to its
correct position we can save it with respect to the map. Does anyone know
if a similar feature exists in ChimeraX ?  Is there a way where the
coordinates .pdb/cif file can be saved with respect to its map in ChimeraX ?

Thank you

-- 
Faisal Tarique Khaja



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[ccp4bb] Off-topic question

[khaja faisal tarique]

Hi everyone,

I was wondering can anyone suggest me how to project the primary sequence
conservation calculated through the Consurf server.  Any help or suggestion
will be appreciated. I have pasted a figure from an article just
for reference.


Best

Khaja

[image: image.png]



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Re: [ccp4bb] Help needed finding hit condition

[khaja faisal tarique]

Hello everyone.

I remember the screen was again from Jenabioscience and this had happened
with one of my protein. The screen was very old and the condition was
peg3350, tris pH 8, lithium sulfate and NaCl as the salt. Hit was obtained
which was never reproducible. Luckily I solved the structure from the hit
itself which diffracted to 2.2A resolution. But it is still a mystery for
us but this is all crystallography is. Strange things happen.

Faisal
Postdoc
PHRI, NJ, USA

On Jul 31, 2017 5:19 PM, "Janet Newman"  wrote:

> ​Hi Jonathan,
>
>
> Hopefully you know about the trick of making any precious condition last
> longer - use the 'magic' solution only in the drop itself, and use the best
> approximation you can make in the reservoir of the experiment (if you are
> doing vapour diffusion)
>
>
> Regards, Janet
>
>
> Janet Newman
> Principal Scientist / Director, Collaborative Crystallisation Centre (C3)
> CSIRO Material Science and Engineering
> 343 Royal Parade
> Parkville.  VIC. 3052
> Australia
> Tel +613 9662 7326 <+61%203%209662%207326>
> Email janet.new...@csiro.au
> --
> *From:* CCP4 bulletin board  on behalf of Jonathan
> Bailey 
> *Sent:* 31 July 2017 22:34
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Help needed finding hit condition
>
>
> Dear CCP4bb community
>
>
> I apologies for the slightly off topic post.
>
>
> We have recently had success crystallizing a membrane protein (diffraction
> > 3 Å at a synchrotron source) using the *in meso* method, the hit
> condition was from the Jena Bioscience screen Pi-minimal condition number
> #57.
>
>
> Hit condition – 47.1 % w/v PEG1000, 150 mM Tris pH 8.0, 80 mM Potassium
> bromide
>
>
> The screen is old and expired 12/20/2013 (lot # JBS00013133), we have
> tried to reproduce the crystals using homemade optimization screens around
> the hit condition but have not had any success. We have tried reproducing
> the hit using a new (not expired) Pi-minimal screen but had no success. We
> are only able to reproduce the crystals using the expired screen and we do
> not have much of it left.
>
>
>
> We went back and tested the pH of the condition that had given crystals,
> the expected pH was 7.9 but we found it to be 6 – 6.5 using a pH indicator
> strip. We believe the drop in pH is caused by oxidative degradation of the
> PEG1000 resulting in the formation of carboxylic acid species.
>
>
> We have contacted Jena Bioscience to try and get some of the old screen
> stock but unfortunately they do not have any.
>
>
> My question is does anyone out there happen to have any expired screen
> stocks of this Pi-minimal condition (#57), ideally from the same lot (lot #
> JB200013133), that they would be willing to send us.
>
>
>
> Does anyone have any advice as to how to reproduce the condition? We’ve
> considered bubbling oxygen through and heating the sample to accelerate the
> oxidation process.
>
>
>
> King Regards
>
>
> Jonathan Bailey (PhD student)
>
>
> Professor Martin Caffrey Lab MS group Trinity College Dublin
>