Re: [phenixbb] MSE MET occupancy issue

28 Feb 2012

      Hi Ming,

I guess it's classical copy-paste error. This should work:

ATOM      7  N  AMSE A  81       7.102  12.859   3.614  0.90 
20.31           N
ATOM      8  CA AMSE A  81       8.211  12.620   2.560  0.90 
23.63           C
ATOM      9  CB AMSE A  81       9.571  13.306   2.815  0.90 
26.76           C
ATOM     10  CG AMSE A  81      10.379  13.756   1.572  0.90 
33.90           C
ATOM     11 SE  AMSE A  81       9.481  15.049   0.267  0.90 
61.25          SE
ATOM     12  CE AMSE A  81       9.069  13.831  -1.266  0.90 
54.62           C
ATOM     13  C  AMSE A  81       8.355  11.286   1.756  0.90 
20.79           C
ATOM     14  O  AMSE A  81       7.994  11.272   0.577  0.90 
21.96           O
ATOM      7  N  BMET A  81       7.102  12.859   3.614  0.10 
20.31           N
ATOM      8  CA BMET A  81       8.211  12.620   2.560  0.10 
23.63           C
ATOM      9  CB BMET A  81       9.571  13.306   2.815  0.10 
26.76           C
ATOM     10  CG BMET A  81      10.379  13.756   1.572  0.10 
33.90           C
ATOM     11  SD BMET A  81       9.481  15.049   0.267  0.10 
61.25           S
ATOM     12  CE BMET A  81       9.069  13.831  -1.266  0.10 
54.62           C
ATOM     13  C  BMET A  81       8.355  11.286   1.756  0.10 
20.79           C
ATOM     14  O  BMET A  81       7.994  11.272   0.577  0.10 
21.96           O

Pavel

On 2/27/12 4:52 PM, Ming wrote:
...
Hi Pavel,
Here is the portion that keeps giving me errors.
Thank you,
ATOM      7  N  AMSE A  81       7.102  12.859   3.614  0.90 
20.31           N
ATOM      8  CA AMSE A  81       8.211  12.620   2.560  0.90 
23.63           C
ATOM      9  CB AMSE A  81       9.571  13.306   2.815  0.90 
26.76           C
ATOM     10  CG AMSE A  81      10.379  13.756   1.572  0.90 
33.90           C
ATOM     11 SE  AMSE A  81       9.481  15.049   0.267  0.90 
61.25          SE
ATOM     12  CE AMSE A  81       9.069  13.831  -1.266  0.90 
54.62           C
ATOM     13  C  AMSE A  81       8.355  11.286   1.756  0.90 
20.79           C
ATOM     14  O  AMSE A  81       7.994  11.272   0.577  0.90 
21.96           O
ATOM      7  N  BMET A  81       7.102  12.859   3.614  0.10 
20.31           N
ATOM      8  CA BMET A  81       8.211  12.620   2.560  0.10 
23.63           C
ATOM      9  CB BMET A  81       9.571  13.306   2.815  0.10 
26.76           C
ATOM     10  CG BMET A  81      10.379  13.756   1.572  0.10 
33.90           C
ATOM     11  SG BMET A  81       9.481  15.049   0.267  0.10 
61.25           S
ATOM     12  CE BMET A  81       9.069  13.831  -1.266  0.10 
54.62           C
ATOM     13  C  BMET A  81       8.355  11.286   1.756  0.10 
20.79           C
ATOM     14  O  BMET A  81       7.994  11.272   0.577  0.10 
21.96           O
On Mon, Feb 27, 2012 at 5:12 PM, Pavel Afonine mailto:[email protected]> wrote:
Hi Ming,
can you send me the PDB file or its portion that still results in
    problem?
Pavel
On 2/27/12 1:47 PM, Ming wrote:
...
Hi all,
I was trying to refine a protein with phenix.refine. I want to
    refine AMSE and BMET with occupancies 0.5 and 0.5.
    What I did is modifying the pdb file by copy the coordinates of
    MET to MSE, and change the names to be AMSE and BMET, modifying
    the occupancy to be 0.5 and 0.5 for each one. Everything else
    like the atom names have been taken care of too. I used the
    readyset to make sure the pdb file is good. But phenix.refine
    keeps giving me error saying "numbers of atoms with unknown
    nonbonded energy type symbols ". Anyone here can help me with
    this please?
    Thanks in advance,