[chimerax-users] Secondary structure display - pdb and cif

[Greg Couch]

Phenix used to have, and maybe still does, a problem with generating 
mmCIF files. In several places, it outputted the author sequence number, 
auth_seq_id, where it should put the label sequence number, 
label_seq_id.  Tristan Croll has already reported one version of this 
bug to Phenix about 5 months ago, 
https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2483.  Perhaps there is 
a newer version of Phenix that has the bug fixed?  And is that the 
mistake you make when you generate the mmCIF from the PDB file 
yourself?  You should be able to tell by looking at the atom_site table 
and the label_seq_id's for the various residues and see how that matches 
up to the beg_label_seq_id and end_label_seq_id values in the 
struct_conf table.  The size of the complex is not an issue.  If that's 
not the bug, then send me the complete mmCIF file and I'll guess what 
the bug is.


     HTH,

     Greg


On 3/4/2020 12:58 AM, Tetter Stephan wrote:
>
> Dear  all,
>
>
> I am having an issue with secondary structure display. I am real-space 
> refining a set of 120 chains in phenix. Of these, only 10 are unique, 
> the rest is symmetry-related. Thus, I define secondary structure 
> elements for the 10 unique chains only. The output pdb file header 
> contains the secondary structure elements as imposed during 
> refinement. Displaying this pdb file in ChimeraX shows the right 
> secondary structure. The mmcif file instead, whether I use the phenix 
> output or generate it from the pdb myself, displays different, 
> non-sensical structures. Secondary structure is shown in loop regions, 
> and some actual strands and helices not recognized at all. This 
> artifact is only shown for the 10 subunits with secondary structure 
> definitions, the other subunits show no secondary structure at all, 
> thus something is read in, but not correctly, apparently. Any idea 
> what the problem could be? Could the size of the complex be an issue?
>
>
> The attachments show the lines from the two file types concerning 
> secondary structure definitions.
>
>
> Kind regards,
>
>
> Stephan
>
>
>
>
>
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