Re: Same residues look different
Hi Adinda, You will get answers faster if you send your questions to the list, so keep it in CC. đ I also observe this difference in coloring when using the button or your command. Note that the log reports a slightly different command when using the toolbar button. But I don't know why these two commands produce such different results. Try reading the documentation (the command "help coulombic" will open the relevant page). Regarding your second question, this is explained in the documentation (and in physical chemistry textbooks): "Coulombic electrostatic potential is calculated from atomic partial charges and coordinates according to Coulomb's law: Ï = ÎŁ [qi / (Δdi)] Ï is the potential (which varies in space), q are the atomic partial charges, d are the distances from the atoms, and Δ is the dielectric, representing screening by the medium. The resulting potential is in units of kcal/(mol·e) at 298 K. A distance-dependent dielectric is sometimes used to approximate screening by implicit solvent. By default, distDep true and dielectric 4.0 are used" What is represented on the surface of the protein as a red-blue gradient are the values of this electrostatic potential, which is continuous in space. So, your example aromatic residue appears blue because there must be a positively charged residue sufficiently close in space (look around, you should find it). This is not too surprising: lysine and arginine often make cation-pi interactions with aromatic residues. See https://en.wikipedia.org/wiki/Cation%E2%80%93%CF%80_interaction for more info. I hope this helps, Guillaume ________________________________ From: ADINDA <adinda.fitri.falinka@gmail.com> Sent: Friday, July 12, 2024 9:27:12 AM To: Guillaume Gaullier Subject: Re: [chimerax-users] Same residues look different Dear Dr Guillaume, Thank you for your prompt response. I have another question. * How does the ESP colouring work? When you click on molecular display and click "electrostatic" after that, it shows you the charges on the surface protein display (blue for positive, red for negative). But if you run the command "coulombic protein surfaces #sample", you'll get a different view, with the positive and negative parts becoming more pronounced. <https://preview.redd.it/need-help-with-chimerax-v0-loexjv50glbd1.png?width=5...> [r/labrats - this is the view I get when I just click electrostatic in the molecular display bar (PDB: 2j1a)] this is the view I get when I just click electrostatic in the molecular display bar (PDB: 2j1a) <https://preview.redd.it/need-help-with-chimerax-v0-vmusn036glbd1.png?width=1...> [r/labrats - this is what I get when I run the command "coulombic protein surfaces" (PDB: 2j1a)] this is what I get when I run the command "coulombic protein surfaces" (PDB: 2j1a) * Why is tryptophan/phenylalanine (actually any hydrophobic a.a for that matter) "positively charged" when I turn on ESP? (it's coloured blue when it should be white) <https://preview.redd.it/need-help-with-chimerax-v0-3fmfb2rjglbd1.png?width=6...> [r/labrats - my mouse is hovering at the light blue area next to phenylalanine label] my mouse is hovering at the light blue area next to phenylalanine label Best, Adinda On Fri, Jul 12, 2024 at 2:50âŻPM Guillaume Gaullier <guillaume.gaullier@kemi.uu.se<mailto:guillaume.gaullier@kemi.uu.se>> wrote: Hello Adinda, These two lysines look different because one displays the hydrogen atoms while the other one doesnât. The one that doesnât show them probably doesnât have them in the coordinate file (omitting them is a common practice when doing model building), but you can add them with the command "addh". Once they are added, or with a coordinate file that already had them, you can hide them from the display with the commande "hide H". The other reason these two lysines look different is because they have different rotamer conformations. As far as I can tell, they seem to be from different structures, so this is normal. These conformations depend on the underlying experimental data that were used to build these atomic models (an electron density map from a crystallographic dataset, or a cryoEM map). If you display the map overlayed on the atomic model, you can determine how well these rotamers are supported by the data. But lysines exposed at the surface, like these ones, often show poor density (because they are flexible), so the rotamer modeled in the atomic model is unlikely to fully account for the real conformations. I hope this helps, Guillaume On 12 Jul 2024, at 06:35, ADINDA via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear developers, I have a few questions about how residues are visualised on your software. <image.png> <image.png> They're both lysine but look different. What can I do to solve this? Best, Adinda VARNING: Klicka inte pĂ„ lĂ€nkar och öppna inte bilagor om du inte kĂ€nner igen avsĂ€ndaren och vet att innehĂ„llet Ă€r sĂ€kert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ NĂ€r du har kontakt med oss pĂ„ Uppsala universitet med e-post sĂ„ innebĂ€r det att vi behandlar dina personuppgifter. För att lĂ€sa mer om hur vi gör det kan du lĂ€sa hĂ€r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy VARNING: Klicka inte pĂ„ lĂ€nkar och öppna inte bilagor om du inte kĂ€nner igen avsĂ€ndaren och vet att innehĂ„llet Ă€r sĂ€kert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.
Hi Adinda, Your second surface (mostly red) looks wrong. Just use the icon or the same "coulombic" command that is shown in the Log when you use the icon. I have no idea what #28 is in your system or why you would use the "surfaces" option. In most cases people will not use the "surfaces" option of coulombic; it is only for specialized situations. Options are explained in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coulombic.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 12, 2024, at 6:15 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Adinda,
You will get answers faster if you send your questions to the list, so keep it in CC. đ
I also observe this difference in coloring when using the button or your command. Note that the log reports a slightly different command when using the toolbar button. But I don't know why these two commands produce such different results. Try reading the documentation (the command "help coulombic" will open the relevant page).
Regarding your second question, this is explained in the documentation (and in physical chemistry textbooks):
"Coulombic electrostatic potential is calculated from atomic partial charges and coordinates according to Coulomb's law: Ï = ÎŁ [qi / (Δdi)] Ï is the potential (which varies in space), q are the atomic partial charges, d are the distances from the atoms, and Δ is the dielectric, representing screening by the medium. The resulting potential is in units of kcal/(mol·e) at 298 K. A distance-dependent dielectric is sometimes used to approximate screening by implicit solvent. By default, distDep true and dielectric 4.0 are used"
What is represented on the surface of the protein as a red-blue gradient are the values of this electrostatic potential, which is continuous in space. So, your example aromatic residue appears blue because there must be a positively charged residue sufficiently close in space (look around, you should find it). This is not too surprising: lysine and arginine often make cation-pi interactions with aromatic residues. See https://en.wikipedia.org/wiki/Cation%E2%80%93%CF%80_interactionfor more info.
I hope this helps,
Guillaume
From: ADINDA <adinda.fitri.falinka@gmail.com> Sent: Friday, July 12, 2024 9:27:12 AM To: Guillaume Gaullier Subject: Re: [chimerax-users] Same residues look different
Dear Dr Guillaume, Thank you for your prompt response. I have another question. âą How does the ESP colouring work? When you click on molecular display and click "electrostatic" after that, it shows you the charges on the surface protein display (blue for positive, red for negative). But if you run the command "coulombic protein surfaces #sample", you'll get a different view, with the positive and negative parts becoming more pronounced.
this is the view I get when I just click electrostatic in the molecular display bar (PDB: 2j1a)
this is what I get when I run the command "coulombic protein surfaces" (PDB: 2j1a) âą Why is tryptophan/phenylalanine (actually any hydrophobic a.a for that matter) "positively charged" when I turn on ESP? (it's coloured blue when it should be white)
my mouse is hovering at the light blue area next to phenylalanine label Best, Adinda
On Fri, Jul 12, 2024 at 2:50âŻPM Guillaume Gaullier <guillaume.gaullier@kemi.uu.se> wrote: Hello Adinda,
These two lysines look different because one displays the hydrogen atoms while the other one doesnât. The one that doesnât show them probably doesnât have them in the coordinate file (omitting them is a common practice when doing model building), but you can add them with the command "addh". Once they are added, or with a coordinate file that already had them, you can hide them from the display with the commande "hide H".
The other reason these two lysines look different is because they have different rotamer conformations. As far as I can tell, they seem to be from different structures, so this is normal. These conformations depend on the underlying experimental data that were used to build these atomic models (an electron density map from a crystallographic dataset, or a cryoEM map). If you display the map overlayed on the atomic model, you can determine how well these rotamers are supported by the data. But lysines exposed at the surface, like these ones, often show poor density (because they are flexible), so the rotamer modeled in the atomic model is unlikely to fully account for the real conformations.
I hope this helps,
Guillaume
On 12 Jul 2024, at 06:35, ADINDA via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear developers, I have a few questions about how residues are visualised on your software. <image.png> <image.png> They're both lysine but look different. What can I do to solve this? Best, Adinda
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participants (2)
-
Elaine Meng -
Guillaume Gaullier