Friday, November 20, 2009

Registered COPPA Users in phpBB3

Recently, I received an email from a 3DNA user who registered at the 3DNA forum, but could not see anything at all once logged in. 3DNA forum is based on phpBB3, and has been running for over three years now. So at the very beginning, I thought how could it be? I had never heard of any such problem/complain from 3DNA forum registers before. I even created a temporary test login account and found no problem. So I communicated with the user and asked her/him to log in using my test account, and again everything was fine!

To reproduce the problem, I logged in as the user, and found one thing spurious: the user was in the group of "Registered COPPA Users", not the normal "Registered Users". I did not know what that COPPA stands for. So I googled the phase "Registered COPPA users" and the top hit led me into the phpBB3 document on Group Management, and the section I am interested in reads as follows:
Registered COPPA users are basically the same as registered users, except that they fall under the COPPA, or Child Online Privacy Protection Act, law, meaning that they are under the age of 13 in the U.S.A. Managing the permissions this usergroup has is important in protecting these users. COPPA doesn't apply to users living outside of the U.S.A. and can be disabled altogether.

So a registered COPPA user is, by definition, under the age of 13. By default phpBB3 does not even allow such a child to read any content! In the context of 3DNA forum, this policy simply does not make any sense — the contents (in the public section) are viewable by any one without registration.

It turned out that at registration stage, the first question is: "To continue with the registration procedure please tell us when you were born." Two dynamically generated dates are given, one is "Before" a date defining an age over 13, and the other "On or after" it for below 13. Obviously the 3DNA user mentioned above clicked the wrong button.

After knowing where the problem was and how it was created, fixing it was straightforward. Interestingly, when I then checked the 3DNA forum registered users, I found five of them were in the "Registered COPPA Users" group. Obviously, the previous (wrong) registers did not complain — possibly lost interest in pursuing further, so this issue did not surfaced until recently.

In a real world as we live, what seems simple may not be. Nothing should be taken for granted.


As mentioned previously, PDB makes use of blocview (part of 3DNA) to generate the simple yet effective images for nucleic-acid-containing structures. That's the connection I knew of between 3DNA and PDB. By pure chance, however, I recently noticed the 3DNA entry in PDB — it is actually a protein structure, completely unrelated to the 3DNA software package!

Just out of curiosity, I browsed the abstract of the Liu et al. article, titled "Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I...S and I...Se halogen-bonding" [J Mol Biol. 2009 Jan 16;385(2):595-605]. I then downloaded the full PDF version of the paper and read it carefully through. This work studied binding interactions of benzenes with the internal cavity of L99A mutated T4 lysozyme. The authors demonstrated that the center of the phenyl ring can be shifted by more than one angstrom due to different halogen-substitutions (where the 3DNA entry corresponds to C6H5I), and (further) proved the concept that "the protein is flexible and adapts to the size and shape of the ligand". At better than 2.0 Å resolution, they also observed the I...S and I...Se halogen-bonds.

I became interested in this paper not just because of the name of 3DNA, for which a quick browsing over the abstract would be sufficient. This paper also reminded me of an early article I published with the title "Influence of fluorine on aromatic interactions":
Non-covalent interactions between aromatic ligands influence the conformations of metal complexes, and the system [M(OAr)2L2] has been used to investigate the difference between phenyl–phenyl, phenyl–pentafluorophenyl and pentafluorophenyl–pentafluorophenyl interactions. X-Ray crystal structures show that pentafluorophenyl groups adopt partially stacked orientations with the two aromatic rings close to parallel and with significant π overlap. In contrast, phenyl groups are skewed away from each other with only edge-to-face contacts. Phenyl–pentafluorophenyl interactions adopt a coplanar fully stacked geometry. These results have been rationalised on the basis of energy calculations (carried out blind) using a variety of empirical models for treating weak non-covalent interactions. The major cause of the different behaviour of the three systems lies in the electrostatic interactions between the π systems.

Knowing of the pattern of a PDB id, — 4 characters long: the first character is a numeral in the range 0-9, while the rest can be either numerals or letters — I played around with some other possible ids with my name initials in it. Indeed I found one, 1XJL, a protein structure of human annexin A2 in the presence of calcium ions. If you are bimolecular structure-oriented, why not have a try with some ids of special meaning to you — you might be related to PDB in some unexpected way!