[chimerax-users] Saving PDB file as a string

[Sophie Liu]

Hi Eric,

The information really is at the end of the file after “TER” like.

Thank you so much for the information. I would really appreciate anymore
guidance you can give.

I really just need to be able to access the PDB in its entire text format
or in some form that I can iterate through.

Best,
Sophie

On Tue, Jun 7, 2022 at 8:32 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Sophie,
> The normal PDB reader does not preserve the full text of the PDB file as
> is.  In particular, nothing in the "coordinates" section of the file (ATOM
> records and beyond) is preserved as text -- it is translated into data
> structures.  Lines above the coordinates section are preserved in the
> 'metadata' attribute of the structure.  For a PDB file, the metadata would
> be a dictionary keyed on record type (*e.g.* 'JRNL') with a corresponding
> value of a list of lines of that record type.  So if the information you
> are looking for is in the header lines then you are good to go.  If the the
> information really is "at the end of the file" like you said, then you
> would need to implement your own reader that preserves that information.
> Let me know if you really need that and I will provide further guidance.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Jun 7, 2022, at 3:20 PM, Sophie Liu via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Hi,
>
> My organization has some extra information at the end of a PDB file that I
> would like to be printed onto the Log Console of ChimeraX.
>
> I am currently writing a bundle to do so by adding a command (however if
> this is best implemented by overriding the open command for PDB files then
> I would switch to that).
>
> I am wondering how I can have the bundle work like so:
> 1. the user types a command call it, "showdata"
> 2. the bundle would read all Models (that are pdb files) that are being
> displayed
> 3. for each model it would read the PDB text file, and say go to indices
> 200-251 of the string and display that in the Log console
>
> I hope this makes sense. I am mainly struggling on how to access the
> original PDB text of the model.
>
> Best,
> Sophie
>
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