PDB deposits

Robert W. Harrison harrison at calvin.jci.tju.edu
Thu Nov 3 15:07:51 EST 1994

In article <1994Nov1.155703.31821 at cc.usu.edu>, slszc at cc.usu.edu writes:
|> 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?

Often alpha carbons only means that the structure has problems, or is
a preliminary trace and the authors (quite rightly) don't want to
deposit a highly suspect structure.   Sometimes it is a commercially
funded structure (such as HIV-RT) and then only the minimum is 
allowed by the funders to be deposited.

|> > 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

1) ftp.pdb.bnl.gov  (anonymous FTP, username = anonymous, password
                     = your mail address)
   email them at pdb at bnl.gov
2)  try "man ftp" :-) (help on vax'es)
3) The way i do it is to get the index files "?????.idx" and
then search them with grep on my home machine.  If you use
"grep -i <string> <file>" then you don't have to worry about
upper case.  It also helps to have an idea who did the structure.
There are also a bunch of perl/awk scripts for this search, and
the instructions are given somewhere.  

4) Retreive the newsletters for much more complete information.

			hope the helps.

					robert w. harrison
					harrison at asterix.jci.tju.edu
					fax (215) 923 2117

Organic chemistry is the chemistry of carbon compounds.
Biochemistry is the study of carbon compounds that crawl.
                -- Mike Adams

When in doubt, use brute force.
                -- Ken Thompson

When we are planning for posterity, we ought to remember that virtue is
not hereditary.
                -- Thomas Paine

For every complex problem, there is a solution that is simple, neat,
and wrong.
                -- H. L. Mencken


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