Hi Paul, the format of the file got screwed. I am resending the file in the attachment. I would like to repeat the description of the problem. There is a difference in recording of water molecules in coot and in phenix. The example is given in the attached pdb file. I apologize for the wrong subject (pointer distances), as this was my previous request to make pointer distances available to atoms of symmetry molecules. Maia Maia Cherney wrote:
Thank you, Paul.
There is also difference in recording water. Should it be ATOM or HETATM? Phenix makes it HETATM, but coot makes it ATOM.
Here is an example that was saved after adding one water molecule in coot (after refinement in phenix).
HETATM10472 O HOH S1252 75.727 6.379 70.023 1.00 31.17 O HETATM10473 O HOH S1253 40.692 -0.062 54.840 1.00 37.64 O TER 10474 HOH S1253 ATOM 10475 O HOH S1254 75.842 2.043 56.024 1.00 35.64 O TER 10476 HOH S1254 END
Maia
Paul Emsley wrote:
Maia Cherney wrote:
Hi Paul,
Coot saves pdb files with TER card. The problem is the TER card takes the next atom number.
ATOM 2303 C4 ADP A 288 33.070 4.240 14.161 1.00 11.08 C TER 2304 ADP A 288 ATOM 2305 O SER B -1
The same model after phenix gives no number to the TER card.
ATOM 2303 C4 ADP A 288 33.070 4.240 14.161 1.00 11.08 C TER ATOM 2304 O SER B -1
As a result, the number of atoms in the pdb files is different. That is confusing. Could you please fix this problem.
Maia
Hi Maia,
It seems to us that this is an issue with Phenix, not Coot or mmdb.
Have a look here:
http://www.wwpdb.org/documentation/format32/sect9.html#TER
"The serial number of the TER record is one number greater than the serial number of the ATOM/HETATM preceding the TER"
Regards, Paul.