On 04/22/2013 08:16 AM, Paul Emsley wrote:
On 21/04/13 01:49, Jinzhong Lin wrote:
Dear Coot users,
I have been refining the crystal structure of a large assembly which
has half a million of atoms. In the PDB, when atom number exceeds
99999, it starts to use letters such as A0000. Everything was fine
for phenix and coot to deal with such a structure until recently I
tried to refine the TLS parameters. The TLS refinement puts ANISOU
record below each ATOM line in the PDB file and when the atom number
has 5 digits it concatenates with ANISOU giving something like:
ATOM 99999 O2* Cr A 453 41.217 18.570 115.721
1.00107.41 16S1 O
ANISOU99999 O2* Cr A 453 18694 11085 11032 -1586 395
-1101 16S1 O
ATOM A0000 C1* Cr A 453 42.986 17.740 114.321
1.00106.92 16S1 C
ANISOUA0000 C1* Cr A 453 18592 11040 10992 -1526 256
-1044 16S1 C
When I try to open the PDB file in coot, it gives an error:
ERROR 14 READ: Unmatch in different records for the same atom.
LINE #200536
ANISOUA0000 C1* Cr A 453 18592 11040 10992 -1526 256
-1044 16S1 C
It looks like coot does not recognize ANISOU followed by a letter
without space in between. (ANISOU99999 is fine)
I am not sure if it is a bug of coot or it is inherited from mmdb. I
would appreciate it very much if anyone can help me out or give me a
clue.
I believe that this is an mmdb issue. I will inform Eugene (if he
doesn't already know about and has fixed it already).
Regards,
Paul.
Thanks a lot. I am currently using Nat's way to remove the records
before I load it into Coot.
Best,
Lithlin
