The full biological unit should be available in biological assembly file.
Have you tried using the fetch command?
i.e.:
fetch 1avd, type=pdb1
set all_states, on
The first retrieves BA #1, the all_states shows the models.
If there is something wrong with the assembly file - then by all means
c
CONECT records are not used for peptide bonds for standard amino acid and
nucleic acid links. These are assumed. In addition, for these standard
chemical component, CONECT records are not used to internal bonds - they
are "known."
Non standard amino/nucleic acids used CONECT records for all atoms
1hho does have a non-standard crystal frame. (see remark 285)
If you load the assembly PDB file in rasmol - it displays properly. Pymol
is having the issue.
However, if you fetch the cif file in pymol, and ask it to display the
assembly - it does the right thing.
set assembly, 1
fetch 1hho
Ezr
As long as you update the external source package (and all
dependencies) to python 2, I have no objection. I feel that pymol is a
moving target and if you need the latest and greatest tools, use them.
My only concern is performance. If moving to python 2 has a
performance hit, then I would be conce
PDB format dictates that TER records are present at the end of a polymer chain.
Chain breaks or non-sequential numbering do not introduce TER records. A TER
record is required between the polymer and non-polymer chain - even with same
chain ID. TER records should not be between non-polymers...
The dots and question marks are appropriate. You did not export a PDB
file, but instead an mmCIF/PDBx file.
For an explanation of what the fields mean, you can look at
http://mmcif.wwpdb.org/docs/tutorials/content/atomic-description.html
On 1/21/20 9:46 PM, Ofir Shein Lumbroso wrote:
Hi all
