Ralf W. Grosse-Kunstleve wrote:
I.e. the first 9 serial numbers are represented as usual. The
following atoms use a base-36 system (10 digits + 26 letters) with
upper-case letters. 43670016 (26*36**4) additional atoms can be
numbered this way. If there are more than 43770015 (9+43670016)
DeLano
Sent: Thursday, August 09, 2007 5:53 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB format survey?
Joe,
I feel that atom serial numbers are particularly important, since
they, combined with CONECT records, provide the only semi-standard
convention I know
is to maintain as much interoperability as possible.
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On
Behalf Of Santarsiero, Bernard D.
Sent: Friday, August 10, 2007 8:17 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] PDB format survey?
Can I ask a dumb
8:17 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] PDB format survey?
Can I ask a dumb question? Just curious...
Why are we now limited to 80 columns? In the old days, that
was a limit with Fortran and punched cards. Can a record
(whatever it's called now) be as long as we wish
-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On
Behalf Of Warren DeLano
Sent: Thursday, August 09, 2007 5:53 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB format survey?
Joe,
I feel that atom serial numbers are particularly important,
since they, combined
Dear George,
I like your hybrid_ 36 scheme and will implement it and the two character
hain IDs PDB file columns 21 and 22, right justified) when I next update
HELXL. Of course I will need to do some programming because of the SHELX
zero dependency' philosophy, but it seems to me to be
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB format survey?
Joe,
I feel that atom serial numbers are particularly important, since
they, combined with CONECT records, provide the only semi-standard
convention I know of for reliably encoding bond valences
information
Dear Ralf,
I like your hybrid_ 36 scheme and will implement it and the two character
chain IDs PDB file columns 21 and 22, right justified) when I next update
SHELXL. Of course I will need to do some programming because of the SHELX
'zero dependency' philosophy, but it seems to me to be
I support CCP4 adopting the hybrid36 and 2 char chain id extensions too.
If no-one else steps up to do it, I'll try and patch mmdb to support it
when I get time.
Kevin
George M. Sheldrick wrote:
I like your hybrid_ 36 scheme and will implement it and the two character
chain IDs PDB file
On Wednesday 08 August 2007 20:47, Ralf W. Grosse-Kunstleve wrote:
The solution to this problem is to simply treat the serial numbers and
residue numbers as strings. X-PLOR/CNS has been doing this forever,
maybe other programs, too.
Implementations to generate intuitive, maximally backward
Hi Ethan,
Is that A a hexidecimal number, or is it a decimal number
that just happens to have an A in front of it?
[A-Z][0-] gives a larger range of values than 5 bytes of hexadecimal,
so I'm guessing it's the former. But the example is not clear.
(yes I could download and inspect
Edward A. Berry wrote:
Ethan A Merritt wrote:
On Wednesday 08 August 2007 20:47, Ralf W. Grosse-Kunstleve wrote:
Implementations to generate intuitive, maximally backward compatible
numbers can be found here:
http://cci.lbl.gov/hybrid_36/
From that URL:
ATOM 8 SD MET L
standard set of hacks we all agree upon by
supporting them in our code.
Cheers,
Warren
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Joe Krahn
Sent: Thursday, August 09, 2007 1:15 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB format survey?
Edward
bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Joe
Krahn
Sent: Wednesday, August 01, 2007 5:17 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB format survey?
Ethan Merritt wrote:
Examples include:
- very large structures, for which the current 80 column PDB format
runs out of space
Does it matter what the PDB use? They will export PDB and mmCIF for us
to use, so what they use internally doesn't matter. (IIUC the EBI uses SQL).
From my perspective as a developer I am not bothered in the slightest
whether we use PDB or mmCIF, because I read everything through MMDB
which
So, I am thinking about putting up a survey somewhere to get a measure
of the user-communities interests, because RCSB and wwPDB seem
uninterested in doing so. Maybe a group result would be more useful in
influencing the standards. I am hoping that the wwPDB can become a
better place for format
On Wednesday 01 August 2007 14:10, Joe Krahn wrote:
In addition to questions about the PDB standard, it is probably
important to consider mmCIF. One thing I don't like about it is that
columns can be randomized (i.e. X, Y, and Z can be in any column), but
the mmCIF standards people have no
organic firewall,
-Tom
-Original Message-
From: CCP4 bulletin board on behalf of Ethan Merritt
Sent: Wed 8/1/2007 3:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB format survey?
On Wednesday 01 August 2007 14:10, Joe Krahn wrote:
In addition to questions about the PDB standard
Ethan Merritt wrote:
Examples include:
- very large structures, for which the current 80 column PDB format
runs out of space for atom numbers (4 columns - max )
or for chain ids (1 column - single char A-Z 0-9)
[don't ask my why they don't want lower case]
- new classes of
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