PDB deposits

slszc at cc.usu.edu slszc at cc.usu.edu
Tue Nov 1 16:57:03 EST 1994


In article <Aigo0cm00iVC86V2sG at andrew.cmu.edu>, Stewart Buskirk <sb86+ at andrew.cmu.edu> writes:
> 
>     As a new grad student learning crystallography, I've been spending
> some time finding interesting structure reports and then trying to get
> the coordinates from PDB to examine the structure in more detail.
> 
>     Unfortunately, I have found that a significant number of published
> reports, many over a year old, have not had the corresponding
> coordinates sent to PDB!  And many of the ones that have been entered
> consist solely of the alpha-carbon coordinates.
> 
>     I plead with you to tell me why - are people just being secretive?
> Is PDB making unreasonable demands on submitters? Are they going
> somewhere else? Is making coordinates available no longer customary?
> 
>     One of my concerns is that some papers that report novel tertiary
> structures based on *review of PDB structures* do not submit their own
> coordinates!  
> 
>     I would appreciate any/all comments that could shed some light on
> this situation for me.  I would like to understand the role of
> coordinate publication in structure reports and get a better handle on
> the limitations of the PDB.
> 
>     Thank you!
> 
> 
> ***************************************************************************
> 
> Stewart Buskirk                                 Computers
> PhD candidate, Dept. of Biological Sciences         +      =  Discovery!
> Carnegie Mellon University                       Biology
> 4400 Fifth Ave.
> Pittsburgh, PA   
>                  412-244-9874    sb86 at andrew.cmu.edu
> ***************************************************************************
As a new graduate student I havent even reached this level of sophistication
could someone please give me a tutorial as to :
1. What is the ftp site for brookhaven protein data bank?
2. How to down load files from the bank?
3. How if I dont have the filename can i search for the coordinates for
lignin peroxidase structure.
For some reason none in my university are able to help.

thanks in advance.

Adi
slszc at cc.usu.edu




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