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<p class="MsoNormal">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.</p>
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<p class="MsoNormal">Thanks again,</p>
<p class="MsoNormal">Arthur</p>
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<p class="MsoNormal" style="border:none;padding:0cm"><b>De: </b><a href="mailto:meng@cgl.ucsf.edu">Elaine Meng</a><br>
<b>Enviado:</b>quarta-feira, 5 de maio de 2021 21:54<br>
<b>Para: </b><a href="mailto:arthurpfonseca3k@hotmail.com">Arthur Pereira da Fonseca</a><br>
<b>Cc:</b><a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>
<b>Assunto: </b>Re: [Chimera-users] Contact in angstrom</p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Hi Arthur,<br>
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.<br>
<br>
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.<br>
<br>
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.<br>
<br>
11 contacts<br>
atom1 atom2 overlap distance<br>
ASP 236.A OD1 BGC 310.A O3 0.414 2.466<br>
ASN 91.A OD1 BGC 310.A O6 0.360 2.520<br>
ARG 158.A NH1 BGC 310.A O2 0.312 2.788<br>
ASP 236.A OD2 BGC 310.A O2 0.289 2.591<br>
HIS 152.A NE2 BGC 310.A O6 0.266 2.834<br>
ASP 154.A OD1 BGC 310.A O1 0.231 2.649<br>
ASP 14.A OD1 BGC 310.A O4 0.230 2.650<br>
ASN 211.A ND2 BGC 310.A O3 0.072 3.028<br>
ASN 91.A ND2 BGC 310.A O5 0.065 3.035<br>
TYR 10.A CE2 BGC 310.A C6 0.018 3.622<br>
ASP 236.A CG BGC 310.A O2 0.005 3.335<br>
<br>
...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.<br>
<br>
16 contacts<br>
atom1 atom2 overlap distance<br>
ASP 236.A OD1 BGC 310.A O3 0.414 2.466<br>
ASN 91.A OD1 BGC 310.A O6 0.360 2.520<br>
ARG 158.A NH1 BGC 310.A O2 0.312 2.788<br>
ASP 236.A OD2 BGC 310.A O2 0.289 2.591<br>
HIS 152.A NE2 BGC 310.A O6 0.266 2.834<br>
ASP 154.A OD1 BGC 310.A O1 0.231 2.649<br>
ASP 14.A OD1 BGC 310.A O4 0.230 2.650<br>
ASN 211.A ND2 BGC 310.A O3 0.072 3.028<br>
ASN 91.A ND2 BGC 310.A O5 0.065 3.035<br>
TYR 10.A CE2 BGC 310.A C6 0.018 3.622<br>
ASP 236.A CG BGC 310.A O2 0.005 3.335<br>
ASN 256.A ND2 BGC 310.A O1 -0.005 3.105<br>
ASN 91.A OD1 BGC 310.A C6 -0.022 3.322<br>
ASN 211.A CB BGC 310.A O3 -0.030 3.370<br>
ASP 154.A OD1 BGC 310.A C1 -0.038 3.338<br>
ASP 14.A CG BGC 310.A O4 -0.083 3.423<br>
<br>
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.<br>
<br>
ChimeraX Contacts tool has the option "Find pairs of atoms with center-center distance..."<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html">https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html</a>><br>
<br>
ChimeraX "contacts" command has the option "distanceOnly"<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html#distanceOnly">https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html#distanceOnly</a>><br>
<br>
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.<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On May 4, 2021, at 2:12 PM, Arthur Pereira da Fonseca <arthurpfonseca3k@hotmail.com> wrote:<br>
> <br>
> 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:<br>
> <br>
> findclash :.A test :. B overlap -0.4 hbond 0.0 namingStyle simple save<br>
> <br>
> However I don’t know exactly how to modify the overlap to the desired distances.<br>
> <br>
> Which values can I use to measure contacts within 2, 3 and 4 Å.<br>
> <br>
> Thanks in advance,<br>
> Arthur Pereira <o:p></o:p></p>
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