Zhijie I have fixed both these bugs and you should be able to download the next nightly build to run ReadySet! on your file. In the meantime, I'm happy to run ReadySet! on your model. Make sure you send it off list. Nigel NB. Any files sent to me will be held in strictest confidence. On Mon, Apr 29, 2013 at 4:42 PM, Zhijie Li wrote:

** 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 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

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