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If you don't want scala to keep your Bijvoet-pairs separate, you
should uncheck the appropriate button in the ccp4i-GUI. However, since
you have SIGF_New, your mtz-file already contains the merged
Bijvoet-pairs.
Scala is not a refinement programm and
Note that Scala Aimless always put I+, I- and Imean into the output file,
which then get propagated through [c]truncate. This is irrespective of whether
the Anomalous data flag is switched on: that only affects outlier rejection and
some statistics. Note also that Aimless (recent versions
Francois,
I did not realize Phil Evans is god (perhaps a minor one as he did not
yet earn a capital G).
I do concur that insertion code is evil. I had to re-refine an old
antibody structure recently and it messes up coot sequence window and
breaks refmac bond restraints. Evil, evil,.evil.
not god I don't think I wrote that bit!
Phil
On 5 Dec 2012, at 15:06, Ed Pozharski wrote:
Francois,
I did not realize Phil Evans is god (perhaps a minor one as he did not
yet earn a capital G).
I do concur that insertion code is evil. I had to re-refine an old
antibody structure
The last time I tried the pdbset renumber command because of issues with
insertion codes in certain programs, it failed to also renumber the LINK,
SSBOND CISPEP records. Needless to say, thanking god (or even God) was
not my first thought! (more along the lines of why can't software
developers
Hi Ian,
It's easy to forget about LINK records and such when dealing with the
coordinates (I recently had to fix a bug in my own code for that).
The problem with insertion codes is that they are very poorly defined in the
PDB standard. Does 128A come before or after 128? There is no strict rule
I had always assumed that ASCII sort order was the standard so ' 128A'
comes after ' 128 ' in the collating sequence, and indeed the PDB
documentation seems to make it clear that it comes after, e.g. in the
section describing the ATOM record:
REFERENCE PROTEIN NUMBERINGHOMOLOGOUS
Dear All,
I repost this message on behalf of Dr. Jia-huai Wang, as this position needs to
be filled as soon as possible. For inquiries please contact Dr. Wang directly
at jw...@red.dfci.harvard.edu
Postdoctoral Position in Structural Biology of Immune Receptors:
There is an immediate opening
Hi Robbie,
On Wed, 2012-12-05 at 17:02 +0100, Robbie Joosten wrote:
Hi Ian,
It's easy to forget about LINK records and such when dealing with the
coordinates (I recently had to fix a bug in my own code for that).
The problem with insertion codes is that they are very poorly defined in the
On Wed, 2012-12-05 at 17:02 +0100, Robbie Joosten wrote:
Does 128A come before or after 128?
Robbie,
shouldn't it simply depend on which residue record comes first in the
pdb file?
Ed.
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Dear Jiawei,
Thanks for spotting this and bringing it to our attention. It is a serious bug
in the interface when using the default protocol for Acorn. When running Acorn
to determine heavy atoms the default is to truncate the resolution to 3.5
Angstroms. However this default is there for all
Hi Ian,
The 'standard' you describe below is more of a suggestion than a rule. The
PDB does not enforce a numbering scheme which is particularly annoying when
dealing with engineered proteins with linkers or domains of different
proteins (they come with all sorts of numbering schemes). Of course,
The Marletta Lab at The Scripps Research Institute is looking for a
postdoctoral fellow to study the structure and function of Heme- Nitric
Oxide/Oxygen binding (H-NOX) domains, a family of gas sensing proteins that are
prevalent in prokaryotes and higher eukaryotes. The ideal candidate will
Hi Peter,
Thanks for the info. I'd better go check whether my code assumes insertion
codes are not digits.
Cheers,
Robbie
Date: Wed, 5 Dec 2012 17:57:58 +
From: pkel...@globalphasing.com
Subject: Re: [ccp4bb] thanks god for pdbset
To: CCP4BB@JISCMAIL.AC.UK
Hi Robbie,
On Wed,
I would like to call your attention to a BBSRC-funded PhD studentship in the
lab of Doryen Bubeck at Imperial College London starting October 2013.
Title: Complement-mediated pore formation
The immune complement system in blood kills microbes by making ‘membrane-attack
complex’ (MAC) pores in
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