before modelling a long side-chain in non-existing or dubious density,
also make sure it is really there in the protein by sequencing your
expression plasmid. Your arginine (for example) may in fact be a
serine or glycine...databases are not 100% accurate and neither is PCR
if it was used i
OK, here we go again.
This has been argued ad nauseam, see for example
http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19738.html
or
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg20268.html
(hard to believe we have gone more than a year without another version
of "what to do with diso
CP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] side chain density
Dear Remy and Faisal -
Just a geeky bioinformatics note: searching my local copy of the PDB
(somewhat out of date), shows that 22,165 out of 72,000 structures
contain a 'REMARK 470' line, which is how the PDB notes that at
Dear Remy and Faisal -
Just a geeky bioinformatics note: searching my local copy of the PDB
(somewhat out of date), shows that 22,165 out of 72,000 structures
contain a 'REMARK 470' line, which is how the PDB notes that atoms are
missing from a residue. Some of these are no doubt mistakes by
Dear Faisal,
You definitely do not mutate to alanine as that would imply for the
future "user" of your pdb file that it is a mutant.
Some people feel they have to keep the side chain but put the
occupancies at zero. I think this is a bad practice and strongly oppose
to it as for the future "u
On Friday, 09 November 2012, Faisal Tarique wrote:
> Dear all
>
> i have solved a structure ( at 2A resolution) whose Rwork and Rfree is 22
> and 25 respectively..the Ramachandran plot shows 90% of the residues in the
> most favorable region and with 6 residues in generously allowed and no
> resid
Hi,
There has been quite a lot of discussion about this and I think
different opinions exist. I would try to keep the side chains, if
there is some evidence where they are. Otherwise I would just delete
atoms and I would not mutate them to alanine.
http://www.mail-archive.com/ccp4bb@jiscm
Dear all
i have solved a structure ( at 2A resolution) whose Rwork and Rfree is 22
and 25 respectively..the Ramachandran plot shows 90% of the residues in the
most favorable region and with 6 residues in generously allowed and no
residues in disallowed region. But in some areas i can see density m
