Dear all,
Best wishes for the new year!
I am looking for some statistics about the fraction of protein structures in
the pdb that are actually crystallized with a His tag, and from those
crystallized with a His tag whether these construct were engineered with a
cleavable tag or not. Has an
I vaguely remember a paper by Aled Edwards, where they did the statistics for
their targets at SGC. As far as I recall they engineer with cleavable tag
purify and cyrstallize it first with tag and only if they don't get crystals or
a structure they cleave off the tag and rerun the screens. I thi
It is normal for me, expressed a few proteins before and mass conformed all MET
is SE-met. DQ
From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Yibin Lin
[yyb...@gmail.com]
Sent: Thursday, January 06, 2011 3:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Sub
Hi Kenneth,
There are recognized advantages to including riding hydrogens during
refinement, even at low resolution. Others have written on this better than I
could (the following link is a post to the CCP4bb from the archives):
http://www.ysbl.york.ac.uk/ccp4bb/2002/msg01215.html
-An
The RCSB PDB site (www.pdb.org) provides as sequence motif search as an
advanced search option. For example to search for a N-terminal (His)6 tag, use
the following regular expression:
^HH
or HH to find any sequence with a (His)6 pattern.
Click on this link to retrieve all seq
Obviously, this depends a bit on which refinement program you use, and I
am not familiar with all of them. However, I have had some
conversations with Garib "refmac" Murshudov and Pavel "phenix.refine"
Afonine about this, and the shocking answer appears to be "no". Carbon
has six electrons, e
Hi,all
I refined a protein-ligand complex structure using Refmac5 and got the map
coefficient "A.mtz" file. I want to represent the electron density in Pymol,
so I transformed "A.mtz" into "A.map" ccp4-format map file using FFT in
ccp4i (parameters are: generate "simple" map in "CCP4" format to co
Hi, Nian,
Thanks for your reply. I figured out the problem just now. The difference
indeed came from my FFT transformation. I just used all default parameters
when I transform "A.mtz" to "A.map", so in the "Run FFT" dialog, F1= F,
Sigma=SIGF, PHI=PHIC, Weight=Unaasigned, and I got "A.map" under th
On Fri, Jan 7, 2011 at 10:49 AM, James Holton wrote:
> But what about MolProbity? and all those neat inter-digitating hydrogens?
> Should it not be possible for the refinement program to be "smarter" about
> where it puts riding hydrogens? Well, that is always possible, but I don't
> think MolP
Hi Zhihong -
You should use 'FWT' and 'PHWT'. These are the sigma-A weighted 2Fo-Fc map
coefficients (likewise, 'DELFWT' and 'PHDELWT' are the sigma-A weighted
Fo-Fc map coefficients). The sigma-A weighted 2Fo-Fc map (also known as the
mFo-DFc map) has become the standard electron density map
On Fri, Jan 7, 2011 at 2:34 PM, Matthew Franklin wrote:
> However, I'm not sure if you're doing the right thing by leaving SIGF
> unassigned. I believe this should be assigned to the experimental error,
> which is usually called 'SIGF' in your mtz file. I don't know if FFT
> actually uses this
Matthew & Nat,
Thanks very much, your answers made me much clear about the map
manipulating, as well as usage of Refmac and FFT. Just from my results, I
think I agree with Nat that "Sigma" and "Weight" is unnecessary when running
FFT based on a Refmac-resulted mtz file, since my "A1.map" is exactl
Dear James,
I did once write a refinement program so I should try to answer your
question. All hydrogen atoms attached to C and N in standard proteins and
almost all in DNSs and RNAs can be calculated geometrically with no
ambiguities. This has been standard practice in SHELX for about 35 years
13 matches
Mail list logo
