Hi Srinivasan,
I always use edstats from the command line: 'edstats.pl HKLIN 101m_0cyc.mtz
XYZIN 101m_0cyc.pdb'. I hadn't noticed it was well-hidden (or the limit case:
not present) in CCP4i. I guess a feature request is in order.
Cheers,
Robbie
Date: Wed, 13 Mar 2013 03:42:45 +0800
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Dear Niu,
could you let us know more about what you have already tried?
- - use more images, maybe all images for indexing
- - try a different program: xds instead of mosflm instead of hkl200
instead of d*trek instead of xds depending what you
I forgot to reply to CCP4BB, but this could be interesting not just for Eugene.
Dear Eugene,
I have a couple of questions about images compression and storage:
1)do someone use it in routine work and does it works well for them?
-Yes, in Utrecht we do routinely compress images (ncompress).
Many thanks for responses!
I will try check and find most convenient for me.
14.03.2013 13:39, Loes Kroon-Batenburg пишет:
I forgot to reply to CCP4BB, but this could be interesting not just
for Eugene.
Dear Eugene,
I have a couple of questions about images compression and storage:
1)do
Dear all,
Twice a year, the Protein Data Bank in Europe (PDBe; http://pdbe.org)
releases new and improved tools and services. Our first website update
of 2013 features:
1. A new weekly overview of new biology in the PDB
2. Improved searching of EMDB entries with rapid filtering of results
Ah yes a new logo...
But it might be of interest to hear in this forum what has happened to the CCP4
logo that used to appear on the PISA and Fold pages in acknowledgement of the
support from the BBSRC on the underlying algorithms for these services.
It is only by acknowledgement of the
Ed, no the fact that you don't, can't or won't estimate the precision
doesn't change anything (only as you say it becomes a poorly designed
experiment). A measurement has a standard deviation regardless of whether
you possess an estimate of its value or not. The exact true value of the
standard
Dear CCP4users biologists,
I'm trying to get a CNS solve v1.3 profit license.
I don’t know how to contact person who deals with CNS profit license.
Could you give the hint for getting the license or authorization for CNS
program?
Kind regards,
Genie
Genie
790-784 room 204, Dept of
Dear Martyn,
Numerous external databases, resources and software have contributed
significantly to the quality of the PDBe database and its web
applications. We gratefully acknowledge all these contributions,
including those from CCP4 at:
Dear All
Tomorrow friday the 15th of march is the deadline for registration to
ESS Science Symposium on Neutron Protein Crystallography
to be held at Aarhus University, Denmark
21-22 March 2013
For more info and registration go to http://www.bioxray.au.dk/essprotein
Looking forward to see you
I had a similar situation once where I intentionally collected 5-degree
images from a salt crystal. I found this page:
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Small_molecules
most helpful. Particularly the DELPHI keyword. Thanks to Kay
Diederichs for pointing this out to
4th Edition of the ISBC2013
Dear Colleague,
The Laboratory of Crystallographic Studies is pleased to announce the 4th
International School on Biological Crystallization (ISBC2013), to be held in
Granada (Spain) during May 26-31, 2013. ISBC2013 is intended for
postgraduate/postdoctoral students
Dear colleagues,
we have collected 200 degrees worth of oscillation data on a
selenomethionine derivative (1 non-terminal methionyl per 120 residues)
to 2A resolution.
XDS provides the following output:
COLLECT.LP
LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM DEGREES)
CHARACTER
Dear all,
I am now struggling to align two 3D RNA structures. I know there are a
bunch of web servers, but they either just generated a pdb file with a
single aligned structure, or they left the ligand out.
Does any of you have some recommendations?
Alternatively, is there some software that
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Dear Chen,
lsqman, lsqkab, and most likely coot should be able to do this.
Best,
Tim
On 03/14/2013 09:53 PM, Chen Zhao wrote:
Dear all,
I am now struggling to align two 3D RNA structures. I know there
are a bunch of web servers, but they
Dear Chen,
you can find lsqkab and Topp in ccp4 : coordinates utility and superpose
molecule (if you use the GUI).
Hope to help you.
Nicolas
Le 14/03/13 21:53, Chen Zhao a écrit :
Dear all,
I am now struggling to align two 3D RNA structures. I know there are a
bunch of web servers, but
I would keep the hexagonal lattice, assuming your integration was OK - no
missed spots and then index the data as P1.
If the anom Pattersons should then show the correct symmetry - if the Patterson
shows P6/mmm symmetry you should be safe
in either assigning P6122 or P6522 to the structure SG.
Hi Tim,
I only tried HKL2000, and index with different resolution and different
number of images. I am not quite familiar with XDS or d*trek.
One thing I am not sure is if this large oscillation angle will cause
problem in indexing?
If this is true, any method to overcome it?
The situation I
5 degrees per image may be problematic for some algorithms since the
diffraction spots have uncertain positions in three dimensions. Two dimensions
will come from the position of the spot on the detector and the position of the
detector. The third dimension will come from the rotation angle
I have this question. For exmaple, a protein could be crystallized in two
crystal forms. Two crystal form have same space group, and 1 molecule/asymm.
One crystal form diffracts to 3A with 50% solvent; and the other diffracts to
3.6A with 80% solvent. The cell volume of 3.6A crystal must be
Hi Genie,
I'll ask someone from our Korea office to get in touch with you regarding your
request.
CNS for profit licenses do have to be licensed through Accelrys.
Thanks,
Francisco
Francisco Hernandez-Guzman, PhD
Sr. Product Manager
Accelrys Software, Inc
From: CCP4 bulletin board
I find that least-squares fitting of RNA in coot is fairly painless, robust and
straightforward. It will move all of the contents of one pdb file, not just
the RNA residues you select to align.
On Mar 14, 2013, at 1:53 PM, Chen Zhao chenzhaoh...@gmail.com wrote:
Dear all,
I am now
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