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.
				rob


-- 
					robert w. harrison
					harrison at asterix.jci.tju.edu
					(215)-955-4592
					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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