My suggestion would be to refine with full glu and then put either O and C
atoms at the region corresponidng to the extra electron density.
On Wed, May 18, 2011 at 1:41 PM, Borhani, David <
david.borh...@deshawresearch.com> wrote:
> Glutamate methyl ester? (or ethyl ester, which I’m not sure
Hi Yogesh,
> Could someone help me fix this or point me to other program that could do
> the phase combination similar to SIGMAA?
>
the command:
phenix.reciprocal_space_arrays
is designed to do this (and more). Details:
http://www.phenix-online.org/documentation/reciprocal_space_arrays.htm
Pa
My goal is to combine experimental phases to calculated phases from partial
model. I am using SIGMAA in CCP4, which gave the following error, all labels
that program can not find are present in the input file though.
Error in LABIN: label PHIB not found in file!
Error in LABIN: label FOM not found
Glutamate methyl ester? (or ethyl ester, which I'm not sure has ever been
documented...hard to tell how many extra heavy atoms given the view direction
in the image you supplied). Or the methyl/ethyl amides.
Dave
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bosch,
Juer
Hi All:
I have a structure with two chains in P21212 with cell parameters 85, 123,
51A. Co-crystallization with a ligand results in a new crystal form, and
we collected a data set to 2.3A with cell parameters of 85, 123, and 203A.
There (h,k,4n) spots are all strong, but the remainder are not all
I take the lysine back, just realized wrong color coding it's an oxygen and not
a nitrogen closer to the extra density :-)
Jürgen
On May 18, 2011, at 2:03 PM, Bosch, Juergen wrote:
But that's a lysine, so maybe a PTM ? Acetylated perhaps ?
Jürgen
On May 18, 2011, at 1:56 PM, Shiva Bhowmik wrot
But that's a lysine, so maybe a PTM ? Acetylated perhaps ?
Jürgen
On May 18, 2011, at 1:56 PM, Shiva Bhowmik wrote:
Hi Cedric,
I presume you collected the datset at a synchrtron source. It could be free
radical generated due to X-ray radiation has modified the glutamate residues. I
have seen
Hi Cedric,
I presume you collected the datset at a synchrtron source. It could be free
radical generated due to X-ray radiation has modified the glutamate
residues. I have seen this happening for Ser residues.
Cheers,
Shiva
On Wed, May 18, 2011 at 9:08 AM, cedric bauvois wrote:
> Hi, everyone
Yes, reciprocal lattice coordinates are available for reflections with
d*TREK.
My colleague has also written a "reciprocal lattice viewer" which takes
image pixels and transforms them to a reciprocal lattice. I'm sure others
have similar programs.
But in this modern internet age, I would say enli
Related to manual indexing, >20 years ago I wrote a program to transform a
list of peaks from the original Xentronics detector to points in reciprocal
space. The peaks were written as a PDB file so the peaks (now waters) could
be displayed on any graphics program. It was very useful for seeing and
There are a couple of tricks I know for dealing with datasets that are
problematic to index (ignore if you've tried them):
1. double-check the machine parameters (detector to crystal distance and
beam center in particular).
2. Index in mosflm using widely separated images (usually n,n+45,n+90
Jason,
How does the diffraction pattern look?
Do you see multiple lattices or split spots?
It seems to me that XDS isn't able to index it (correctly) possibly because
of these things.
It's always worth it to manually page through your images just to confirm.
I've personally seen people just use X
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