[Chimera-users] Electrostatic potential molecular surfaces

Wed Sep 11 18:05:43 PDT 2019

Dear Elaine
Thank you for answering some of my questions and answering the email with
several parameters that I did not know.
  I am very grateful for your time.
The questions I have in the future I will send to the group.

I am a big fan of Chimera and I really appreciate your help.

best regards,

Fernando

ATTE
Fernando Villa Díaz

El mié., 11 de sep. de 2019 a la(s) 17:52, Elaine Meng (meng at cgl.ucsf.edu)
escribió:

> Yet another issue I should mention is that in the methods I described, the
> whole amino acid residue is assigned a given kdHydrophobicity value or
> polar/nonpolar classification, not distinguishing between which atoms in
> the residue are more polar than other atoms in the same residue.  To
> distinguish polar vs. nonpolar at the atom level instead of whole residues,
> you’d have to use some other program or approach.
>
> I just remembered another web server not related to Chimera. At  least
> when I tried it many years ago, the results included a column for the
> apolar area:
> <http://curie.utmb.edu/getarea.html>
>
> Elaine
>
> > On Sep 11, 2019, at 3:23 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Hi Fernando,
> > Our resources don’t allow spending much time on consulting with
> individual research projects, sorry, and I can only answer mostly as it
> pertains to Chimera as I don’t know the details of parameters developed by
> other people or other programs.  Also Chimera questions should be sent to
> this mailing list instead of to me directly so that other people can also
> benefit, unless private data are discussed or attached.
> >
> > You found an old script that is really special-purpose, finding the
> surface area that is more red than blue after coloring by electrostatic
> potential.  Note that this would include surface that looks white but has a
> tiny, tiny tint of pinkishness.  Also, the surface area that is more blue
> than red is just the complement of the surface that is more red than blue.
> In other words, if the surface is 75% red>blue then it is 25% blue>red
> because very little if any will be pure white.  They always add up to the
> total surface.  So no, you cannot use these scripts to figure out how much
> of the surface is polar or nonpolar.
> >
> > It  may not matter given the above, but which method, set of charges,
> and what parameter values to use for electrostatic potential (ESP)
> calculations are research decisions that I cannot make for you.  There are
> always tradeoffs, and different people have different opinions, etc.
> >
> > I don’t know python, but your generalization to coloring by
> hydrophobicity by identifying cornflower blue vs.goldenrod might be wrong.
> Red vs. blue is simpler since they are RGB color components.  However, even
> if the color comparison is done correctly, the logical problem is the same,
> they always add up to the whole surface, and nearly white areas will always
> be combined with one side or the other.
> >
> > However, you can get the total surface area given some range of
> hydrophobicity values independent of any coloring.  Hydrophobicity in this
> case is just a constant lookup value for each type of amino acid, according
> to this table (kdHydrophobicity column):
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>
> >
> > You would have to decide yourself which range of values is polar or
> nonpolar, but then you could just select all the residues that are less
> than or more than a certain value, e.g. command:
> >
> > select :/kdHydrophobicity>0.0
> >
> > Alternatively you could just use command:
> >
> > select polar
> > select ~polar
> > …but you might not agree with what amino acids are considered polar, as
> shown in a table in this page:
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/resprop/resprop.html#aacat
> >
> >
> > Then if surface is shown you could add up the area for the selected
> residues, e.g. menu: Tools… Structure Analysis… Attribute Calculator, and
> in that tool calculate attribute named whatever you want for “molecules”
> with Formula:
> >
> > sum(areaSAS.residue)
> >
> > (… or SES instead of SAS, to be compared with the corresponding total
> area given in the Reply Log when you show the surface) with option to
> “Restrict formula domain to current selection” and “Show calculation
> results in Reply Log" turned on, other options turned off, click Apply.
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html
> >
> >
> > Totally separate and not related to Chimera, but I happen to know of
> this web server you might be interested in, for comparing ESP of related
> proteins:
> > <https://pipsa.h-its.org/pipsa/>
> >
> > Best regards,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >> On Sep 11, 2019, at 2:16 PM, Fernando Villa <fer.vdl1928 at gmail.com>
> wrote:
> >>
> >>
> >> Dear Elaine C. Meng, Ph.D
> >>
> >> I have some questions about electrostatic potential molecular surfaces
> and protein comparison.
> >>
> >> 1. The following scripts are added, edited from the redarea.py script
> of link http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts, considering
> that the script allows reading the surface in Å2 colored more red than blue
> area.
> >>
> >> 1. Add scripts:
> >>
> >> Command:
> >>
> >>> open
> >>
> >> -blue_area_03.py
> >>
> >> -cornflowerblue_area_03.py
> >>
> >> -goldenrod_area_02.py
> >>
> >> -red_area_02.py
> >>
> >> (the scripts are attached)
> >>
> >>
> >> 2. I used the following commands:
> >>
> >>> open 4MZ2
> >>
> >>> delete solvent
> >>
> >>> addh
> >>
> >>> addcharge
> >>
> >>> Surface
> >>
> >> coulombic -10 red 0 white 10 blue
> >>
> >>
> >> The electrostatic potential surface is presented by Coulombing coloring
> Surface:
> >>
> >>
> >>
> >> <image.png>
> >> I execute the commands:
> >>
> >>> redarea #0
> >>
> >> red area 3562, total area 5730, ratio 0.6217
> >>
> >>> bluearea #0
> >>
> >> blue area 2168, total area 5730, ratio 0.3783
> >>
> >>
> >> The dominant areas of both colors are obtained.
> >>
> >> The following command is input:
> >>
> >>> rangecolor kdHydrophobicity min cornflowerblue 0 white max goldenrod
> >>
> >>
> >>
> >> <image.png>
> >> Next:
> >>
> >>> cornflowerbluearea # 0
> >>
> >> cornflowerblue area 4109, total area 5730, ratio 0.7171
> >>
> >>
> >>> goldenrodarea # 0
> >>
> >> Goldenrod area 1621, total area 5730, ratio 0.2829
> >>
> >>
> >> So, I believe (I'm not sure):
> >>
> >> Blue area + Red area = PSA ß Is correct?
> >>
> >>          White area = NPSA ß Is correct?
> >>
> >>
> >> So, the real blue and red areas would be (not sure):
> >>
> >>
> >> (Redarea * PSA) / Total surf = Real Red area
> >>
> >> (Bluearea * PSA) / Total surf = Real Blue area
> >>
> >> So:
> >>
> >> Bluearea = 1554.6792
> >>
> >> Redarea = 2554.3208
> >>
> >>
> >> Is this calculation correct?
> >>
> >>
> >> Could I apply these calculations to compare them with other proteins of
> the same family?
> >>
> >> For example:
> >>
> >> Protein members of the immunoglobulin family.
> >>
> >>
> >>
> >> In the Chimera version 1.14, I Download the following programs
> pdb2pqr-windows-bin64-2.1.1
> >>
> >> apbs1.5_win64
> >>
> >> Downloaded from the website: http://www.poissonboltzmann.org
> >>
> >> Next, I assign charges and radii with the following parameters of
> PDB2PQR
> >>
> >>
> >> <image.png>
> >> And I saved the file. Pqr
> >>
> >>
> >> <image.png>
> >> Later I opened the file 001_B4.pqr with Chimera 1.14
> >>
> >>
> >> <image.png>
> >> I use the following command:
> >>
> >>> surface
> >>
> >> And run the APBS interface with the following default parameters:
> >>
> >> <image.png>
> >>
> >> As a result, the color gradient of the molecular surface appeared as
> shown:
> >>
> >>
> >> <image.png>
> >> <image.png>
> >>
> >>
> >> However, my question is:
> >>
> >> Are these parameters correct using the force field PARSE of PDB2PQR?
> Or, is it necessary to use a different force field?
> >>
> >>
> >> Could I apply the scripts:
> >>
> >> -blue_area_03.py
> >>
> >> -cornflowerblue_area_03.py
> >>
> >> -goldenrod_area_02.py
> >>
> >> -red_area_02.py
> >>
> >>
> >> to calculate the redarea and bluearea and compare it with other
> proteins?
> >>
> >>
> >> Is there a script that gives me the correct areas of both red and blue
> colors?
> >>
> >>
> >> Sorry for my long email, as I am new to this area. And I really need
> help.
> >>
> >> I apologize for so many questions.
> >>
> >> I would greatly appreciate your help.
> >>
> >>
> >> Best regards,
> >>
> >> Fer.
> >>
> >>
> >>
> >>
> >>
> <blue_area_03.py><red_area_02.py><goldenrod_area_02.py><cornflowerblue_area_03.py>
> >
>
>
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