On 17-8-2018 18:27, Firdous Tarique wrote:
Hello everyone.
I have a basic question. When a validation report of a coordinate is
generated we often come across a term known as "Too-Close Contacts".
Essentially evey PDB file has at least a few of those.
First of all can somebody please explain me what is the shortest
interatomic distance between the two atoms which is permissible ?
There isn't one number for that. When two atoms get close to each other
the balance of repulsive and attractive forces should get close to zero
(the balance of all forces on one atom should be zero in the static
representation of the dynamic structure; but this is probably
un-achievable). If you do energy minimisation with , for example,
GROMACS or YASARA, you can get at zero summed forces on all atoms, but
these are zero in the force field of these MD/EM softwares. And each
time you use another program (or another force field in the same
program) you get different coordinates by the time all summed forces per
atom are zero.
Most force fields know a limited number of atom times and then define a
few functions that determine the forces between those atom types (see eg
https://swift.cmbi.umcn.nl/teach/B2/bioinf_6.html for a very low-level
introduction). One of those forces is the so called Van der Waals' force
(or when integrated, the Van der Waals' energy). This is a description
of the force between two atoms (actually atom types) as function of
their distance.
What we now do in validation is estimate the shortest distance for which
the repulsive force is 'acceptable'. In WHAT_CHECK we did this by simply
counting in a couple thousand PDB files which which is the frequency of
narrow distance bins for short distances and from that determine which
distance only 1 in 1000 pairs should have. From that we subtract a
safety margin of 0.25-0.4 Angstrom), and any pair of atoms shorter than
that is flagged. Obviously, this is not optimal, but today still the
best we think we can do.
H-atoms are an additional problem as we didn't have many protons
available when WHAT_CHECK was designed. But I assume the people who gave
you your clash list have done something similar using very high
resolution structures.
When dealing with H-atoms you need to separate the riding ones, that
have fixed positions, and the others. The riding ones should worry you
more, especially in the beginning of the refinement. This because fixing
these bumps/clashes requires moving non-H atoms. The other H-atoms often
can be de-clashed by rotating them around the heavy atom they are
attached to.
Next, in this list there are Non-H and H columns list, their
Interatomic distance and Clash overlap. I could see two types of
clashes in my validation report. One in which interatomic distance
between the two atom (one is always a modeled H) ranges from
1.7-2.4A, and clash overlap from 04-1.0. The other in which the
interatomic distance between two atom is greater than 2.2A and the
clash overlap is between 0.4-0.6 (always between two non H-atoms).
I would clearly start addressing the non-H atoms first. With some luck,
de-clashing the non-H atoms will solve the H clashes too.
So my question is that out of so many clashes shown in the list which
are one which actually need to be fixed and can't be ignored specially
because one of my ligand is an amino acid which is showing lots of
these H clashes (interatomic distance less than 1.5A).
If you have a lot of such very bad clashes, you might want to reconsider
the whole refinement, or perhaps even the steps before you started
refining. One suggestion is to see what PDB_REDO can do for you.
Greetings
Gert
(Ps, feel free to send me your coordinates and I will give you my
opinion of-the-list).
Regards
Kahkashan
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