[phenixbb] Phenix eLBOW output cif missing Chi angle information

Nigel Moriarty nwmoriarty at lbl.gov
Fri Oct 2 14:32:17 PDT 2015


Please send me the files directly.

NB. Any files sent to me will be held in strictest confidence.


Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, 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

On Fri, Oct 2, 2015 at 2:24 PM, Xiao Lei <xiaoleiusc at gmail.com> wrote:

> Hi Nigel,
> I did import the restraint (the cif file generated from eLBOW) into coot
> and still has the error issue.
> Thanks
>
> Xiao
> On Oct 2, 2015 1:23 PM, "Nigel Moriarty" <nwmoriarty at lbl.gov> wrote:
>
>> Did you load the restraints dictionary from eLBOW into coot using File ->
>> Import CIF dictionary?
>>
>> Cheers
>>
>> Nigel
>>
>> ---
>> Nigel W. Moriarty
>> Building 33R0349, 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
>>
>> On Fri, Oct 2, 2015 at 12:26 PM, Xiao Lei <xiaoleiusc at gmail.com> wrote:
>>
>>> Hi Phenix BB members,
>>>
>>> I tried to generate restraints of 3-METHYL-BETA-D-ASPARTIC ACID (PDB 3
>>> letter code ACB,
>>> http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=ACB).  I am using
>>> this as a template for D-iso-aspartic acid in my model because I can not
>>> find a 3 letter code for the exact D-iso-aspartic acid (I know for
>>> L-iso-aspartic acid the code is IAS but no code for D-iso-aspartic acid)
>>>
>>> I can search in Phenix eLBOW (Mac Phenix Version 1.10pre) with code ACB
>>> and I can find the code and right compound, I tried to generate restraints
>>> of ACB using eLBOW and I got a cif and pdb output of the compound. However
>>> when I import the compound into coot, delete the methyl group to make the
>>> compound a D-isoAsp, and click "edit chi angles", I receive an error: This
>>> residue does not have assigned torsion/chi angles".  I do not know what I
>>> should do to fix the problem. I thought eLBOW would automatically generate
>>> Chi angles but actually it did not in my case.  I appreciate if you have
>>> any input on this.
>>>
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>>
>>
>>
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