[phenixbb] ReadySet & phenix.refine problem: NAG-Asn with hydrogen atoms

Zhijie Li zhijie.li at utoronto.ca
Mon Apr 29 16:42:27 PDT 2013


Hi Nigel,

Please find the two attached PDB files. One is before ReadySet, the other after.

Zhijie


From: Nigel Moriarty 
Sent: Monday, April 29, 2013 7:36 PM
To: PHENIX user mailing list 
Subject: Re: [phenixbb] ReadySet & phenix.refine problem: NAG-Asn with hydrogen atoms


Can you send me the ASN-NAG PDB file?



On Mon, Apr 29, 2013 at 4:01 PM, Zhijie Li <zhijie.li at utoronto.ca> wrote:

  Hello,

  I am refining my structure with hydrogen atoms on (phenix 1.8.2-1309). The protein contains two Asn-linked GlcNAc. I noticed two problems with respect to the NAG-Asn linkage in the presence of hydrogen atoms:

  1) After running ReadySet (to add hydrogen to the PDB ab initio), the H1 on the NAG is pointing to the amino group of Asn, ie, the NAG seems to be interpreted as in its alpha anomer instead of beta (should be GlcNAc beta1,N-Asn). This is not really a problem as it doesn't seem to affect the refinement.

  2) The H21 in Asn is correctly removed by ReadySet, leaving only H22. However, if I send this PDB to phenix.refine, the refinement will fail almost instantly complaining that H22 of the Asn has an unknown nonbonded energy type symbol. But if I simply change the atom name of H22 to H21, the refinement will proceed to completion with no problem, only leaving an H21 at the position where H22 should be.

  I was not sure what caused this error. So I trimmed my PDBs down to the Asn and NAG only, and fed the small PDB to ReadySet and phenix.refine (with an eff file indicating the NAG-Asn linkage) and got the same behavior: H22 on Asn - error; H21 on Asn - OK. 

  I hope someone can look into this. Thanks in advance.

  Zhijie

  _______________________________________________
  phenixbb mailing list
  phenixbb at phenix-online.org
  http://phenix-online.org/mailman/listinfo/phenixbb







-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov 


--------------------------------------------------------------------------------


_______________________________________________
phenixbb mailing list
phenixbb at phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20130429/0aaeaf3c/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ASN-NAG.pdb
Type: application/octet-stream
Size: 2596 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20130429/0aaeaf3c/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ASN-NAG.updated.pdb
Type: application/octet-stream
Size: 3721 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20130429/0aaeaf3c/attachment-0001.obj>


More information about the phenixbb mailing list