[phenixbb] OXT

[Rife, Christopher L]

Okay, I think I found the problem. After my first round of refinement the pdb file looked like this:
ATOM   1903  N   ALA A 124      -4.693  50.930  27.375  1.00 72.40      A    N
ANISOU 1903  N   ALA A 124     9503   9688   8319   1028    520   1111  A    N
ATOM   1904  CA  ALA A 124      -4.940  50.799  25.947  1.00 75.89      A    C
ANISOU 1904  CA  ALA A 124    10040  10319   8474   1166    544   1164  A    C
ATOM   1905  CB  ALA A 124      -5.775  51.970  25.467  1.00 77.30      A    C
ANISOU 1905  CB  ALA A 124    10130  10588   8653   1211    479   1305  A    C
ATOM   1906  C   ALA A 124      -3.615  50.754  25.196  1.00 75.91      A    C
ANISOU 1906  C   ALA A 124    10074  10346   8421   1311    739   1335  A    C
ATOM   1907  O   ALA A 124      -2.627  51.332  25.645  1.00 75.34      A    O
ANISOU 1907  O   ALA A 124     9892  10148   8588   1315    850   1493  A    O
TER

Then after manual rebuilding in coot, it became:
ATOM    967  N   ALA A 124      -4.693  50.930  27.375  1.00 72.40      A    N  
ANISOU  967  N   ALA A 124     9503   9688   8319   1028    520   1111  A    N  
ATOM    968  CA  ALA A 124      -4.940  50.799  25.947  1.00 75.89      A    C  
ANISOU  968  CA  ALA A 124    10040  10319   8474   1166    544   1164  A    C  
ATOM    969  CB  ALA A 124      -5.775  51.970  25.467  1.00 77.30      A    C  
ANISOU  969  CB  ALA A 124    10130  10588   8653   1211    479   1305  A    C  
ATOM    970  C   ALA A 124      -3.615  50.754  25.196  1.00 75.91      A    C  
ANISOU  970  C   ALA A 124    10074  10346   8421   1311    739   1335  A    C  
ATOM    971  O   ALA A 124      -2.627  51.332  25.645  1.00 75.35      A    O  
ANISOU  971  O   ALA A 124     9892  10148   8588   1315    850   1493  A    O  
TER     972      ALA A 124                                                      
ATOM    973  OXT ALA A 124      -3.513  50.141  24.133  1.00 30.00           O  

So I'm guessing that phenix got confused by the OXT happening after the TER card. Everything looked okay in the .geo file. I will try the next round without the extra TER lines and see if that helps...

Thanks,
Chris 

-----Original Message-----
From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Ralf W. Grosse-Kunstleve
Sent: Friday, May 23, 2008 9:28 AM
To: phenixbb at phenix-online.org
Subject: Re: [phenixbb] OXT

> Should phenix.refine be able to handle OXT?

Yes.

> I find it is moving the OXT atom ~2A from where it should be.

This shouldn't happen unless the atoms the OXT is bonded to are missing
and it is floating around in isolation.
Could you check the OXT bonds in the .geo file? (I hope it is obvious.)
If you send me the fragment of our PDB file with the terminus and maybe
a few residues before that I'll take a look.

Ralf
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