[Jmol-developers] pdb group name alignment

[Miguel H. <mt...@mt...>]

>> There is a related (and for PE very serious for rare PDB files) bug in
>> Chime regarding alignment of group (residue) names. It would be best
>> if Jmol can handle residue names in any alignment of the
>> three-character field, e.g. A__, _A_, __A, PC_, _PC.
>
> The current Jmol implementation would *not* handle this.
>
> However, I do not believe that it will be difficult to change, and I
> don't forsee any negative impact.

Jmol now is more 'flexible' and will accept residue names regardless of
the alignment of the characters. (The spec says that they must be
right-aligned, but Eric says that this sometimes presents problems).

This also had an impact on wildcard behavior ... if the group name is too
short, a wildcard pattern will match as if there were extra spaces at the
beginning and/or the end of the name, as needed. I believe that this
behavior is necessary in order to maintain compatibility.

Examples:
  select [t]   # matches T, does not match +T
  select [?]   # matches all single letters
  select [??]  # matches single and double letters
  select [???] # matches everything
  select [?t]  # matches both T and +T
  select [t?]  # matches T, does not match +T
  select [??t] # matches both T and +T
  select [?t?] # matches both T and +T
  select [t??] # matches T, does not match +T]


Eric and/or Tim and/or Frieda ... If you can, please confirm that this is
the desired behavior.


Miguel