Dear Colleagues,
This exchange is a wonderful illustration of the simple fact that
different scientists
work differently, favoring different approach and different tools. For
some, the latest
and greatest formats and support systems are what they need to be
productive. For
a surprising large number of others, change to new methods is a
pointless distraction
from doing good science. What we need to do as a community is not to
tell one
another how they _must_ do their work, but to listen to one another,
being helpful
where we can, and showing mutual respect where we cannot.
To this end, Frances and I have revived an old idea from 2006 of
creating a format
that looks much like the old PDB format but is 132 columns wide with
more characters
allotted to fields that need them. We re-enabled the WPDB server at
http://biomol.dowling.edu/wpdb which can produce either a 132-column
'PDB' entry or
an 80 column PDB entry based on the mmCIF files on the wwPDB server.
This allows
people who work best with tools such as grep and a simple fixed-field
format to have
most of the newer, larger PDB entries in a wide version of the PDB
format. If you don't
need it, or don't like it, you should not use it. If you have need for
it, and need some
things changed, send us an email, and we'll see what we can do to oblige.
Right now it is on an old, slow server. If there is significant use,
I'll move it
to something bigger and faster.
Regards,
Herbert and Frances Bernstein
On 8/5/13 4:05 PM, Boaz Shaanan wrote:
/Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: [email protected]
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710 /
//
//
/
/
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*From:* Nat Echols [[email protected]]
*Sent:* Monday, August 05, 2013 10:45 PM
*To:* בעז שאנן
*Cc:* [email protected]
*Subject:* Re: [ccp4bb] mmCIF as working format?
On Mon, Aug 5, 2013 at 12:37 PM, Boaz Shaanan <[email protected]
<mailto:[email protected]>> wrote:
There seems to be some kind of a gap between users and developers
as far the eagerness to abandon PDB in favour of mmCIF. I myself
fully agree with Jeffrey about the ease of manipulating PDB's
during work, particularly when encountering unusual circumstances
(and there are many of those, as we all know). And how about
non-crystallographers that are using PDB's for visualization and
understanding how their proteins work? I teach many such students
and it's fairly easy to explain to them where to look in the PDB
for particular pieces of information relevant to the structure. I
can't imagine how they'll cope with the cryptic mmCIF format.
>I think the only gap is between developers and *expert* users - most
of the community simply wants tools and formats that work with a
>minimum of fiddling.
That assumes that you can offer such software, but can you? I doubt
that this goal is reachable (in fact our daily experience proves just
that), with all due respect to you developers.
>Again, if users are having to examine the raw PDB records visually to
find information, this is a failure of the software.
It's not raw, it's easily readable text, very easy to interpret with
very little effort.
Anyway, this discussion is a waste of time. The decision has been
taken, mmCIF will prevail and we (expert and non-expert users) have to
swallow the pill.
Boaz
-Nat
