CONECT record from alternate atom to itself

[Tom Goddard]

Reading the attached PDB file that was written by Chimera 1.10.2 generates many CONECT record errors and then only reads 4 atoms instead of the 84 present in the structure. Chimera 1 reads this same file with no errors.

Summary of problems reading PDB file:

Warnings:
CONECT record from alternate atom to itself: 1
CONECT record from alternate atom to itself: 2
CONECT record from alternate atom to itself: 2
CONECT record from alternate atom to itself: 3
CONECT record from alternate atom to itself: 3
47 messages similar to the above omitted

[Tom Goddard]

The PDB file was written by opening the attached mol2 file in Chimera 1 and using File / Save PDB....

[Tom Goddard]

After removing all the CONECT records from the PDB it still only opens 4 atoms. Looking at the file all the atoms have names H, C, N or O with many atoms having the same name in the same residue. Apparently Chimera 2 is only getting one atom for each name.

[Eric Pettersen]

The PDBio code was using the wrong check for whether the alt loc was specified (was using null, should have been using space)