I have two issues on which I would seek your advice. I am using
The first concerns creating protein structures from scratch. I
select Build > Residue from the menu, and then I select my
desired secondary structure. Then I use the Alt shortcut keys to
add amino acids. Then I select Display > Sequence. The first
amino acid I get will sometimes be numbered 2, or 3, and in one
case the numbering began at residue 22! But never has the first
residue received the CORRECT number, which is of course, 1. This
happens even when I start PyMol fresh, and there are no other
structures loaded which might influence the numbering.
Is this a bug? Or am I doing something wrong?
My second issue concerns edited proteins, and it also relates, in
part, to numbering. Recently, I have been constructing deletion
mutants. Typing "help editing" into the command line gives you a
passage which begins as follows:
> PyMOL has a rudimentary, but quite functional molecular
> editing capability. However, you will need to use an
> to "clean-up" your structures after editing.
(As a quick aside, I'm wondering what a "mimizer" might be. If
this was a typographical error, and the word "minimizer" was meant
instead, that still doesn't help me to understand the meaning of
According to various PyMol displays, removing an amino acid does
nothing more than that. It does not create two objects where
there was one. Now, if I save a PDB file of an edited
polypeptide, things are not so clear. A TER record is inserted
where the residue was deleted. The numbering of residues on each
side of the TER is unaltered. So if you deleted residue 8, for
example, then the TER record is preceded by residue 7 and followed
by residue 9. Using the Select Molecules option will give you one
fragment or the other, but there are apparently no separate names
for these fragments which would allow one to use a join command.
Using Select Objects gives you both fragments as one object.
Looking deeper into the PDB file format specification, I think I
see what the problem might be.
In ATOM records, column 22 can specify an optional "chain
identifier". It can be left blank, according to the
specification, but if it is left blank, the assumption is that
only a single polypeptide is present in the file.
So, which way is PyMol treating this collection of amino acids
after a deletion? As one polypeptide, as suggested by the blank
chain identifier field and the Select Objects result? Or, as two
polypeptides, as suggested by the presence of a TER record and the
Select Molecules result?
I know that other programs that I work with, downstream of PyMol,
have trouble with this ambiguity. For now, I am hand-editing PDB
files. I'm a decent programmer. I can write a clean-up routine
which would delete undesired TER record from PDB files, and
renumber amino acids. But if these functions can (and/or should)
be handled from inside PyMol, I would appreciate knowing how.