Dear all,
I have two low resolution (3.8 A) MAD data sets from two different
space groups. There are 4 copies of my molecule in one space group
and 2 copies in the other. The density-modified maps from these data
sets are poor, but still allow me to build a crude model on them.
All the
Forgot to mention that the NCSs are improper.
On Feb 21, 2007, at 6:22 PM, Jianghai Zhu wrote:
Dear all,
I have two low resolution (3.8 A) MAD data sets from two different
space groups. There are 4 copies of my molecule in one space group
and 2 copies in the other. The density
54 AM, Eleanor Dodson wrote:
You just need one mask for your master molecule, which will be
transferred by the matrices you give to all the other copies.
I make the mask from the crude model, with a generous border round
it - the program will also prune it to get rid of overlaps..
Eleanor
Jia
Dear all,
I have some N-acetyl-glucosamine (NAG) in my structure. When I
searched the monomer library in CCP4 6.0.1, I found out that NAG is
actually N-acetyl-glucose, which is much less common, I believe. I
downloaded the high-resolution structure of N-acetyl-glucosamine from
HIC-UP an
done using libin and there
is a field in the ccp4i for user library)
Garib
On 1 Mar 2007, at 14:07, Jianghai Zhu wrote:
Dear Garib,
NBG is 1-N-acetly-beta-D-glucosamine. However, the sugar
connected to a glycosylation site is actually 2-N-acetyl-D-
glucoamine, which is normally referred as
Dear all,
Sorry for the non-CCP4 question. Does anybody know where the RAMPAGE
server is now? The links I have (http://mordred.bioc.cam.ac.uk/
~rapper/rampage.php and http://mordred.bioc.cam.ac.uk/rampage.php)
don't work anymore.
Thanks.
Jianghai
I am using OS X 10.4.10, G4 powerbook. I have no problem with Kay's
emails, just got a message with "Unable to verify message signature".
Jianghai
On Jul 7, 2007, at 12:38 PM, James Stroud wrote:
Hello All,
I'm not trying to pick on Kay Diederichs here, but is anyone else
having trouble
Hi all,
I know there are a lot of criteria for water picking. It depends on
the resolution, data quality, etc... Can somebody point me a good
literature on this topic? Thanks.
Jianghai
+++
Jianghai Zhu, Ph.D
CBR Institute for Biomedical Research
Department
rmsCHIRAL
0.015 1.150 0.004
The R and Rfree are very similar from these two versions of refmac5.
Does refmac5.4 have different geometry weights from refmac5.3? Which
one is more reasonable?
Thanks.
Jianghai
+++
Jianghai Zhu, Ph.D
CBR
Hi All,
I have a data set with experimental phases. I would like to shift the
origin of the phases so that it matches the origin of another data set
and phases, which has different cell constants. Any suggestion of
what tools has the ability to do this? i.e. shift the origin by (0.0,
0
shift the origin of
phases to
match another set ---
http://solve.lanl.gov/Resolve/html_resolve_manual/resolve_sample_scripts.htm#offset_phases
Regards,
Mitch
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf
Of Jianghai Zhu
Sent: Friday, June 06, 2008 9:
x27;ll only work though if the cell constants are close enough that
you can actually merge the MTZ's sensibly. If that is not the case,
you are really looking at a cross-crystal averaging calculation.
Jianghai Zhu wrote:
Hi All,
I have a data set with experimental phases. I would like to
put MTZ box appears.
It'll work out the shift for you, as long as you have some sort of
phases for both cases.
This'll only work though if the cell constants are close enough that
you can actually merge the MTZ's sensibly. If that is not the case,
you are really looking at a cross-
ived from the origin shifted pdb as
the reference. Now the reference phases and experimental phases have
the same cell constants and space group, the resulting origin shifted
experimental phases will not be distorted.
-- Jianghai
On Jun 6, 2008, at 12:01 PM, Jianghai Zhu wrote:
Hi All
the group associated with each lattice-point. It is the
amplitude, at unit distance, of the wave scattered by the unit group
of s points."
-- Jianghai
++++
Jianghai Zhu, PhD
Immune Disease Institute
Dept. of Pathology
Harvard Medical School
3 Blackfan Circle, CLSB
Bost
With best wishes,
Gerard.
--
On Mon, Jan 12, 2009 at 12:58:27PM -0500, Jianghai Zhu wrote:
JPK beats me on this one. Here is the quote from R. W. James, "The
Optical
Principles of the Diffraction of X-rays".
"We shall call A the 'structure amplitude', a nam
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