[Chimera-users] RES: Contact in angstrom

Thu May 6 09:40:01 PDT 2021

Thanks Elaine. The reason I was using Chimera contacts is because I also thought this is a better measure than simply distances. But I’m just an employee, and if my bosses tell me to use angstroms I have to obey. So I guess I’ll be checking on ChimeraX.

Thanks again,
Arthur

De: Elaine Meng<mailto:meng at cgl.ucsf.edu>
Enviado:quarta-feira, 5 de maio de 2021 21:54
Para: Arthur Pereira da Fonseca<mailto:arthurpfonseca3k at hotmail.com>
Cc:chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>
Assunto: Re: [Chimera-users] Contact in angstrom

Hi Arthur,
The overlap is distance between VDW spheres, so 0.0 overlap means the VDW surfaces are touching.  However, that will be a shorter distance for atoms with smaller VDW radii and a longer distance atoms with larger VDW radii.  I believe the "overlap" is a smarter measure of true contacts than a simple single distance cutoff that doesn't care that atoms are different sizes.  We recommend values for measuring contacts as overlap cutoff in the range 0 to -1, and hbond allowance 0.0.

However, if you really want to use simple center-center distance, if using Chimera (ChimeraX has an option, see below) you would have to manually filter the results by distance.  Since single overlap value is different distance cutoffs for different atoms, so you would want to set a permissive (more negative) overlap and then screen out the contacts with distances that are above that.  The results, which you can show in the Log or save to a file, include the center-center distance in the last column.

For example, if I open glucose-binding protein (2gbp) and identify contacts with overlap cutoff 0 and hbond allowance 0, I get the following.  There are 7 distances <3 and 4 distances >3.

11 contacts
atom1  atom2  overlap  distance
ASP 236.A OD1  BGC 310.A O3  0.414  2.466
ASN 91.A OD1   BGC 310.A O6  0.360  2.520
ARG 158.A NH1  BGC 310.A O2  0.312  2.788
ASP 236.A OD2  BGC 310.A O2  0.289  2.591
HIS 152.A NE2  BGC 310.A O6  0.266  2.834
ASP 154.A OD1  BGC 310.A O1  0.231  2.649
ASP 14.A OD1   BGC 310.A O4  0.230  2.650
ASN 211.A ND2  BGC 310.A O3  0.072  3.028
ASN 91.A ND2   BGC 310.A O5  0.065  3.035
TYR 10.A CE2   BGC 310.A C6  0.018  3.622
ASP 236.A CG   BGC 310.A O2  0.005  3.335

...or if I use overlap cutoff -.1 hbond allowance 0, then the following.  You get the same 7 distances <3 and 4 distances >3 as above, plus  5 more distances >3.  To find even longer distances use a more negative overlap.

16 contacts
atom1  atom2  overlap  distance
ASP 236.A OD1  BGC 310.A O3  0.414  2.466
ASN 91.A OD1   BGC 310.A O6  0.360  2.520
ARG 158.A NH1  BGC 310.A O2  0.312  2.788
ASP 236.A OD2  BGC 310.A O2  0.289  2.591
HIS 152.A NE2  BGC 310.A O6  0.266  2.834
ASP 154.A OD1  BGC 310.A O1  0.231  2.649
ASP 14.A OD1   BGC 310.A O4  0.230  2.650
ASN 211.A ND2  BGC 310.A O3  0.072  3.028
ASN 91.A ND2   BGC 310.A O5  0.065  3.035
TYR 10.A CE2   BGC 310.A C6  0.018  3.622
ASP 236.A CG   BGC 310.A O2  0.005  3.335
ASN 256.A ND2  BGC 310.A O1  -0.005  3.105
ASN 91.A OD1   BGC 310.A C6  -0.022  3.322
ASN 211.A CB   BGC 310.A O3  -0.030  3.370
ASP 154.A OD1  BGC 310.A C1  -0.038  3.338
ASP 14.A CG    BGC 310.A O4  -0.083  3.423

Even though we tried to do a better analysis by using an overlap cutoff instead of a simple single distance cutoff, lots of people got confused about it, so ChimeraX has an option to do that instead.

ChimeraX Contacts tool has the option "Find pairs of atoms with center-center distance..."
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html>

ChimeraX "contacts" command has the option "distanceOnly"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html#distanceOnly>

We are only actively developing ChimeraX now, and you would have to use that program to use that option, as there are no plans to add it to Chimera.
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 4, 2021, at 2:12 PM, Arthur Pereira da Fonseca <arthurpfonseca3k at hotmail.com> wrote:
>
> Hello, I’m trying to measure contacts between a protein and a peptide using Chimera. I have to do this with different angstroms distances, 2, 3 and 4 Å. I'm using the command line:
>
> findclash :.A test :. B overlap -0.4 hbond 0.0 namingStyle simple save
>
> However I don’t know exactly how to modify the overlap to the desired distances.
>
> Which values can I use to measure contacts within 2, 3 and 4 Å.
>
> Thanks in advance,
> Arthur Pereira

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