[chimerax-users] Saving PDB file as a string

[Eric Pettersen]

Great!  I was going to suggest moving that information into the header section somehow as much easier than writing a custom PDB reader, so I'm glad you found some alternative that works.

--Eric

> On Jun 8, 2022, at 6:48 AM, Sophie Liu via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Eric,
> 
> I ended up figuring an alternate implementation, and I can now retrieve the information I want.
> 
> Thank you so much for the help/pointers!
> 
> Best,
> Sophie 
> 
> On Tue, Jun 7, 2022 at 11:07 PM Sophie Liu <sophiel2 at andrew.cmu.edu <mailto:sophiel2 at andrew.cmu.edu>> wrote:
> 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 <mailto: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 <mailto: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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