Re: [Jmol-users] visualizing channels in proteins

[Angel H. <ang...@ua...>]

Hi Karsten
I think you should definitely let Jmol do the work, using the "cavities" option of isosurface. That should not have breaks, as it is calculated using the rolling water probe.

On the other hand, in the paper t¡you quote they say they use Jmol for display, so you could export their result saving the state and bring it back to your page. Or grab their PyMol scripts, which J(S)mol wuld read.

ughhhh..... the server they cite is dead 🙁

"The extracted channels and their properties are displayed within the browser using Java/JMol based applets. PyMOL [38<https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0545-9#ref-CR38>] scripts for individual channels are also generated and may be downloaded for detailed off-line study. "



________________________________
De: Theis, Karsten W. <kt...@we...>
Enviado: sábado, 16 de septiembre de 2023 17:06
Para: jmo...@li... <jmo...@li...>
Asunto: Re: [Jmol-users] visualizing channels in proteins

ATENCIÓN: Este correo electrónico se envió desde fuera de la UAH. No haga clic en enlaces ni abra archivos adjuntos a menos que reconozca al remitente y sepa que el contenido es seguro.
Addendum:

Eric just emailed me, suggesting I check out "isosurface minset 1000 cavity".

Another way is to show slices parallel to the membrane; if you make slice selection interactive, that might be a bit easier to understand. For porin on Proteopedia<https://proteopedia.org/wiki/index.php/Porin#visualizing%20channels>, I made an animated GIF from Jmol images that scan through the slices, and show a pseudo-atom based interactive Jmol scene next to it.

Also, I checked the literature. A 2015 paper<https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0545-9> has a nice overview about dedicated software packages unrelated to Jmol.
[https://media.springernature.com/w200/springer-static/cover/journal/12859.jpg]<https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0545-9>
CHEXVIS: a tool for molecular channel extraction and visualization - BMC Bioinformatics<https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0545-9>
bmcbioinformatics.biomedcentral.com


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Karsten Theis
Chemical & Physical Sciences Department
Westfield State College
________________________________
From: Theis, Karsten W.
Sent: Saturday, September 16, 2023 10:46
To: jmo...@li... <jmo...@li...>
Subject: visualizing channels in proteins

Hi,

I am trying to visualize the channel in aquaporin1, 1IH5. I used Eric Martz's PACUPP<https://proteopedia.org/w/PACUPP> scripts to get the residues lining the channel, and now wanted to use that selection to make a surface showing the channel. My best result so far was with a command such as this:

select 13 , 14 , 17 , 21 , 24 , 25 , 28 , 29 , 32 , 33 , 35 , 37 , 49 , 52 , 53 , 56 , 57 , 60 , 61 , 65 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 , 79 , 80 , 83 , 84 , 87 , 96 , 97 , 100 , 101 , 105 , 120 , 126 , 127 , 128 , 149 , 152 , 153 , 154 , 156 , 157 , 168 , 169 , 171 , 172 , 173 , 175 , 176 , 180 , 183 , 184 , 185 , 186 , 187 , 189 , 190 , 191 , 192 , 193 , 194 , 195

isosurface insideout molecular slab plane (151:A.C)(62:A.O)(81:A.CA) slab plane (50:A.N)(210:A.NE1)(126:A.NH1)

This shows the channel, slabbed at both entrances, with the outside of the channel (which is the inside of the protein) lit up. However, I get some artifact surface patches because some of the atoms I selected to define the channel are also on the outer surface of the protein.

Is there an established way to show channels in Jmol? I see two ways of getting rid of the outer surface patches. I could more carefully select the lining atoms (I just took the residue numbers from Eric's output, not atom by atom). Or I could "bathe" the protein in fake atoms to push out the outer surface so it would no longer show. Or a combination of both.

I'd be happy to learn a better way,
Karsten

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Karsten Theis
Chemical & Physical Sciences Department
Westfield State College