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

Nigel Moriarty nwmoriarty at lbl.gov
Mon Apr 29 17:04:53 PDT 2013


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 <zhijie.li at utoronto.ca> wrote:

> **
> Hi Nigel,
>
> Please find the two attached PDB files. One is before ReadySet, the other
> after.
>
> Zhijie
>
>  *From:* Nigel Moriarty <nwmoriarty at lbl.gov>
> *Sent:* Monday, April 29, 2013 7:36 PM
> *To:* PHENIX user mailing list <phenixbb at phenix-online.org>
> *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
>>
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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 : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>
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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 : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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