[Chimera-users] Contact area between 2 Proteins

Fri May 17 12:20:14 PDT 2019

The help that you have given me has generated great advances in my project
and knowledge about the Chimera 1.13.1 program.

I have a question about the functions mentioned above:
again if I run the tutorial of measure burried area in this case (SAS):

Command: open 1avx
Command: ~ longbond
Command: split
*Command*: *delete*
<https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html>
* solvent*
Command: surface
Command: color sea green # 0.1
Command: color medium purple # 0.2
command: measure buriedArea # 0.1 # 0.2
SAS
Command: color yellow #0.1@/buriedSASArea> 1
Command: color hot pink #0.2@/buriedSASArea> 1
[image: image.png]

*Command*: *alias*
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
*  ^face-me  **set independent*
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#independent>
*;  **turn*
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>
* y -90 model  #0.1; **turn*
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>
* y 90 model  #0.2; **~set independent*
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#independent>

*Command*: *alias*
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
*  ^separate  **move
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>*
* x $1 model  #0.2; **center*
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/center.html>

*Command*: *savepos
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html>*
* closed*

*Command*: *face-me*
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html#aliases>

*Command*: *separate*
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html#aliases>
* 18*

*Command*: *savepos
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html>*
* open*

*surface > hide*
[image: image.png]

  Could I know which residues participate in the interaction with a command
line or a script (.py)?

for not select manually the residues (to avoid this tedious part)

I would greatly appreciate your help!

best regards!

ATTE
Fernando Villa Díaz

El vie., 10 de may. de 2019 a la(s) 15:20, Elaine Meng (meng at cgl.ucsf.edu)
escribió:

> As I already said in the previous message,  if the purpose is to get a
> buried surface area value for atomic structures (not just to make a
> figure), then use “measure buriedArea”:
>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea
> >
>
> The other two methods don’t calculate SAS or SES values, and you said you
> wanted buried SAS.
>
> The “measure buriedArea” command does not have a cutoff parameter.  Just
> make sure to specify only the proteins in the command so that water, etc.
> will not affect the calculation.
>
> Elaine
>
> > On May 10, 2019, at 1:01 PM, Fernando Villa <fer.vdl1928 at gmail.com>
> wrote:
> >
> > Dear Elaine C. Meng ... Thank you very much for the help, and I am more
> clear, the differences between the methods before mentioned.
> > So, if I want to calculate the contact area between two proteins
> (solvent accesible surface area)
> >
> >
> >
> > <image.png>
> >
> > <image.png>
> > <image.png>
> > Is it correct to use a 2.5A cuttoff?
> > which of the three methods should I use?
> > Method 1 (used for the figures) identifies atom-atom contacts with Find
> Clashes/Contacts or its command equivalent, findclash.
> >
> > With the proteins in the bound state:
> >
> > Command: findclash  #0.1  test #0.2  intersub true  overlap  -1  hb 0
> make false  select true
> > Command: namesel contacts
> > Command: ~select
> > Command: color yellow contacts&#0.1
> > Command: color hot pink contacts&#0.2
> > In the findclash command, the overlap and hb parameters are adjustable,
> with values of 0.0-(–1.0) Å and 0.0 Å, respectively, recommended for
> finding contacts. An overlap cutoff of –1.0 identifies pairs of atoms with
> VDW surfaces up to 1.0 Å apart. When the command is instead used to find
> only clashes (unfavorable, too-close contacts), hb values > 0.0 help to
> exclude H-bonding atom pairs. The two sets of atoms are specified with
> model numbers (e.g. #0.1), but chain identifiers could have been used
> instead (e.g. :.a), and if water had not been deleted, the calculation
> could have been limited explicitly to protein (e.g. #0.1&protein or
> :.a&protein).
> >
> > Method 2 first calculates buried surface area, then uses the resulting
> per-atom values (assigned as atom attributes) to identify interface atoms.
> > With the proteins in the bound state:
> > Command: measure buriedArea  #0.1  #0.2
> > Command: color yellow  #0.1@/buriedSESArea>1
> > Command: color hot pink  #0.2@/buriedSESArea>1
> > The total buried area and details of the calculation are given in the
> Reply Log. Different cutoff values could be used, but in this case, atoms
> with > 1.0 Å2 of solvent-excluded surface area buried in the interface are
> similar to the set of atoms found in the method 1 example. Although
> solvent, ions, and ligands are not enclosed in the displayed surfaces, the
> buried-area calculation will include all specified atoms. Thus it is
> important to specify only the intended atoms; for example, if nonprotein
> atoms were present:
> >
> > Command: measure buriedArea  #0.1&protein  #0.2&protein
> > Method 3 identifies where surfaces are close to one another and does not
> involve atoms.
> >
> > With the proteins in the bound state and surfaces shown:
> > Command: measure contactArea  #0.1  #0.2  2.5  color yellow offset 0
> > Command: measure contactArea  #0.2  #0.1  2.5  color hotpink offset 0
> > These commands identify where the surfaces are within 2.5 Å of each
> other. Again, different cutoffs could be used, but 2.5 gave a result
> roughly similar to the preceding examples. The specifications in the
> contact-area command (e.g. #0.1) refer to the surface models, which happen
> to have the same model numbers as the corresponding atomic structures.
> >
> > I apologize to you and the entire community for asking things that may
> be obvious to you and the research community.
> > I am very new in this area and I would be very helpful in completing my
> doctoral thesis.
> >
> >
> > Sincerely, Fernando Villa
> >
> > best regards!
> >
> >
> >
> > El vie., 10 de may. de 2019 a la(s) 10:59, Elaine Meng (
> meng at cgl.ucsf.edu) escribió:
> > Dear Fer Villa,
> > (better to send questions to chimera-users at cgl.ucsf.edu, CC’d here)
> >
> > It is not really a matter of right and wrong.  Instead it depends on
> what you want…
> >
> > If you want to measure buried solvent-accessible and solvent-excluded
> surface areas of atomic structures, use “measure buriedArea”.
> >
> > The “measure contactArea” command is similar but if the goal is
> measurement (rather than coloring for a figure), it is generally used for
> other kinds of surfaces that are not necessarily associated with any atoms,
> like density map isosurfaces.  In that case, the appropriate cutoff value
> really depends on the judgment of the user based on what kinds of surfaces
> these are and what the user is trying to do.
> >
> > The tutorial you mention is for making a figure where the interaction
> surfaces of two proteins are colored, which is a different purpose than
> getting a measurement value.  It explains that different cutoffs could be
> used with “measure contactArea", but the example has 2.5 because it gave
> similar appearance to using the other (buriedArea) method.  The tutorial
> shows both methods because if you are making a figure, you could use either
> one as you like.  It actually discusses three methods.
> >
> > For the other people on the list, here is that tutorial:
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>
> > … 3 methods of coloring the interface:
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html#interface
> >
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > > On May 10, 2019, at 12:17 AM, Fernando Villa <fer.vdl1928 at gmail.com>
> wrote:
> > >
> > > Dear Chimera users,
> > > I would like to know which is the correct method to know what is the
> surface area of contact between two proteins:
> > > measure contactArea or measure buriedArea?
> > > When I apply the command: measure contactArea # 0.1 # 0.2 2.5 color
> yellow offset 0 that comes in the tutorial, it says that the cutting
> distance is equal to 2.5 A2
> > > But, is it correct?
> > > How can I know that?
> > > this example states that if this cut-off distance (2.5 A) is applied
> compared with a cut distance for measure buriedArea:
> > > Command: measure buriedArea # 0.1 # 0.2
> > > Command: color yellow #0.1@/buriedSESArea> 1
> > > Command: color hot pink #0.2@/buriedSESArea> 1
> > > measure buried Area # 0.1 & protein # 0.2 & protein
> > > atoms with> 1.0 Å2
> > > How can I know which is the correct contact area (protein protein
> interaction) of two models or crystals?
> > > What is the correct cutting area that I should apply?
> > > Could it be the default cut area of 1A?
> > > Which method of calculation is better, measure contactArea or measure
> buriedArea?
> > > I would thank you in advance for a possible solution to my problem.
> > >
> > > Best regards.
> > >
> > > Fer Villa.
> > > Enviar comentarios
> > > Historial
> > > Guardadas
> > > Comunidad
> > >
> > > <image.png>
> > >
> > > Command:open 1avx
> > > Command: ~longbond
> > > Command: split
> > > Command: preset apply int 2
> > > Command: repr stick
> > > Command: delete solvent
> > > Command: color sea green #0.1
> > > Command: color medium purple #0.2
> > > Command: surface
> > > Command: measure contactArea  #0.1  #0.2  2.5  color yellow offset 0
> > > Command: measure contactArea  #0.2  #0.1  2.5  color hotpink offset 0
> > >
> > >
> > > or
> > >
> > > Command: measure buriedArea  #0.1  #0.2
> > > Command: color yellow  #0.1@/buriedSESArea>1
> > > Command: color hot pink  #0.2@/buriedSESArea>1
> > >
> > > Command: measure buriedArea  #0.1&protein  #0.2&protein
> > >
> > > ATTE
> > > Fernando Villa Díaz
> > >
> >
> > _______________________________________________
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> > Manage subscription:
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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