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@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