[cctbxbb] Writing a pdb file from an xray_structure object

Claudia Millán Nebot cmncri at ibmb.csic.es
Wed Dec 12 10:47:56 PST 2012


Thank you Pavel :) Therefore i will apply the neccesary transformations
directly on the pdb, and after, i will create the xray structure and work
with it for the next steps. Thanks again!

Claudia Millán (cmncri at ibmb.csic.es)

Institut de Biologia Molecular de Barcelona (IBMB-CSIC)

Barcelona, Spain



2012/12/12 Pavel Afonine <pafonine at lbl.gov>

> Hi Claudia,
>
>
>  i have been using the xray_structure_simple() method to get an
>> xray.structure object from a pdb object and use it to perform some
>> calculations on it, one of them being expand it to P1. After, i tried to
>> write a new pdb out of this xray_structure in P1. For that purpose, i used
>> the following method:
>>
>> cctbx.xray.structure.as_pdb_**file(self, remark=None, remarks=[],
>> fractional_coordinates=False, resname=None, connect=None)
>>
>> but using it both with the original xray structure and with the one on P1
>> I get very bad lookings pdbs, with incorrect formating, like that for the
>> case of the one in P1:
>>
>> ATOM      1 PDB= PDB     1      12.330  -6.948 -40.820  1.00 19.26
>>     N
>> ATOM      2 PDB= PDB     2      49.988  55.370   3.948  1.00 19.26
>>     N
>> ATOM      3 PDB= PDB     3      36.092  30.710  93.483  1.00 19.26
>>     N
>> ATOM      4 PDB= PDB     4      55.370  49.988 175.123  1.00 19.26
>>     N
>> ATOM      5 PDB= PDB     5      30.710  36.092  85.587  1.00 19.26
>>     N
>>
>
> xray_structure object does not have information about
> atom/residue/chain/etc labels. Conceptually, it is supposed to contain
> minimally necessary amount amount of data in order to calculate Fcalc. It
> gets stripped off the moment you go from pdb input object to
> xray_structure_simple().
>
> To write a meaningful PDB file you need to use PDB hierarchy machinery.
> For details, see "cctbx PDB handling tools" article here:
> http://phenix-online.org/**newsletter/CCN_2010_07.pdf<http://phenix-online.org/newsletter/CCN_2010_07.pdf>
>
> There are numerous examples scattered across cctbx code of going back and
> forth between xray_structure object and pdb files.
>
> Pavel
>
> ______________________________**_________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/**mailman/listinfo/cctbxbb<http://phenix-online.org/mailman/listinfo/cctbxbb>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20121212/7f06d729/attachment.htm>


More information about the cctbxbb mailing list