CONECT: where Coot and PyMol collide

Coot is a fantastic program. That’s why most crystallographers use it during their daily tasks.

PyMol is also a fantastic program, with a very simple syntax and easy access to almost all its functions, it is my favorite publication-quality renderer.

I use to jump from coot to pymol and back several times when I prepare my pictures, and I believe that many of you do the same. There is one annoying issue that has been mentioned in the bulletin boards several times (see here and here for example) that is still waiting for a solution.

Let me describe it:

All the PDB files deposited in the Protein Data Bank that contain HET groups interacting with protein atoms, and/or contain disulfide bonds have at their end a section that contains CONECT records. These records strictly depend on the atom numbers involved in the record. Besides these records are an integral part of the PDB file format, in my experience they are hardly ever used fin protein crystallography for particular purposes. And here comes the issue: when you open a PDB file downloaded from the Protein Data Bank with Coot, the program will read the CONECT records, but will NEVER alter them. However, during most editing operations, the atom numbers contained in the file will be modified, and when the changes will be saved, the resulting file will contain a whole set of wrong CONECT records.

Is it a problem?

Well, if you re-open the file with Coot, not at all. But other programs like PyMol or UCSF Chimera consider the CONECT records as an integral part of the information that is read to display the object described in the PDB file.

After saving edits in Coot, a PDB file displayed in PyMol may show a crazy connectivity... This example shows PDB file 2XWB downloaded from the Protein Data Bank withn coot, superposition of chain J to chain A of PDB file 2XW9 (also downloaded from the PDB), modified file saved with Coot and opened subsequently in PyMol

The result?

Have a look at the picture here on the right. The connectivity is quite fancy, isn’t it?

How to solve it?

Here comes the easy part, just delete the CONECT records. But, as this operation is so easy, it becomes tedious if you have to do it manually many many times with a set of files under analysis. And as Coot at the moment does not alter the CONECT records at all (i.e., messes them up after coordinate edits), it would be great if these records were kicked out of the PDB files saved after a Coot editing session.

I’m sure it is in the “todo” list for one of the next Coot versions, I’m just impatient…