Dear Jose,
the question came up again because I did not receive an answer to my
question. The thread discussed benefits and malefits of PDB vs. mmCIF,
which was not my question.
This time, Nat Echolls gave a very reasonable answer (at least for
phenix) on the phenixbb, i.e., that there are no
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On 10/6/2014 4:20 AM, Tim Gruene wrote:
Dear Jose,
the question came up again because I did not receive an answer to
my question. The thread discussed benefits and malefits of PDB vs.
mmCIF, which was not my question. This time, Nat Echolls
Hi all,
reading this beauty I would like to ask a question to the respective
developers:
Will the PDB format remain the working format for the users and only
upon deposition will it be converted to PDBml for archiving purposes, or
are the refinement programs (et al.) going to abandon PDB, too?
Well, if you simply replace that beauty by this one:
grep ^ATOM filename.cif | awk '{print $15}' | awk '{s+=$1;} END {print
s/NR;}'
You will achieve exactly the same result (the b-factors are in the 15th
field of the _atom_site section in deposited mmCIF files). I'm not an
expert in awk,
mmCIF is a very general format with tag-value pairs, and loops
so that tags do not need to be repeated endlessly. It was
designed so that there is the flexibility of defining new terms
easily and presenting the data in any order and with any kind
of spacing.
I understand that there are 10+
On Sun, 5 Oct 2014 13:13:14 +0200, Jose Manuel Duarte jose.dua...@psi.ch
wrote:
Well, if you simply replace that beauty by this one:
grep ^ATOM filename.cif | awk '{print $15}' | awk '{s+=$1;} END {print
s/NR;}'
the problem with this is that it will break if there is any B-factor of 100 or
On Sun, 5 Oct 2014 18:54:16 +0100, Kay Diederichs
kay.diederi...@uni-konstanz.de wrote:
grep ^ATOM filename.cif | awk '{print $15}' | awk '{s+=$1;} END {print
s/NR;}'
the problem with this is that it will break if there is any B-factor of 100 or
higher, because then the blank will be missing
Thanks Frances for the explanation. Indeed mmCIF format is a lot more
complicated and grep can be a dangerous tool to use with them. But for
most cases it can do the job and thus it maintains some sort of
backwards compatibility. I can't agree more that using specialised tools
(for either PDB
