Dear Jinjin Zhang --
On 29 Jul 2008, at 22:34, JINJIN ZHANG wrote:
1. Protein 100 aa, peptide 6 aa, co-crystalized
2. Space group: P43212. Overall R-fac: 0.03. Redundancy: 5 for 98%
of reflections. B-factor:55
3. CNS refinement
4. Phenix xtriage checked, no twinning is suspected.
5. Water
Pointless doesn't do this correctly at present - I need to fix it
For those crystals you are merging into a single dataset, you do need
to decide somehow on a single average unit cell. Pointless attempts to
do this by replacing the cell by the average over all batches within
that dataset,
INVITATION TO PARTICIPATE IN THE TANDEM INSTRUCT WORKSHOP
Intrinsically Unfolded Proteins in Structural Biology”
and
“Complementary Methods in Structural Biology”.
September 4th and 5th, 2008, Hamburg, Germany
The aim of this tandem workshop is to define research areas that should
be covered
Dear Jinjin Zhang,
what happens if you treat your data as perfect twin? Maybe you do have a
twin after all.
Best regards, Daniel
--
Daniel Schlieper email: [EMAIL PROTECTED]
Molecular Motors Group phone: +44 1883 722306 (x 305)
Marie Curie Research Institute
Thank you, Paul and Hidong, for your explanations. Here is another way of
looking at it (kindly provided by Ronald Stenkamp).
===
Think of the electron density as a 3-dimensional function with an average
value of 0.0 (This is true if you have not included an F000 reflection, and
it's true of
Dear P K,
Is it just me or are other people also enjoying the 'name guessing
game' regarding posts to ccp4bb? This one came from
P K [EMAIL PROTECTED]
I could think of a few people with the initials 'P K' - not sure if
everyone is a great biologist (as opposed to just a plain good one).
Dear Snageetha
1) Could you check please if specified atoms have zero occupancy.
Atoms with zero occupancy are considered as absent and there are not
restraints on them
2) symm y at the end of instructions means that the program check all
possible symmetry operators and finds minimal
At the risk of deafness from bees in bonnet (not to mention flogging
dead horses) ...
... the rms value of a Fobs-type map which represents the actual
structure (eg 2mFo - DFc) is _not_ an assessment of the noise level
of the map.
The rms value of a perfect map of this type is function
Dear CCP4 users,
I was using MAPPROT from CCP4 package to rotate/translate an electron
density map in order to superpose maps from different space group
crystals. However, when applying the same operations (euler angles +
translation OR rotation + translation matrices) into the maps and into the
Hi Marko,
On Wed, Jul 30, 2008 at 01:44:48PM +0100, Marko Hyvonen wrote:
Marko Hyvonen
University of Cambridge
[EMAIL PROTECTED]
See: that is an email address I understand .. sort of ... Is that
especially big or very small (in rms/sigma units)?
Cheers
Clemens
--
OK, the first problem is whether you are using maprot in mode 'from' or
'to'. Depending on which you are using, the operators may be the inverse
of what you expect.
The second problem arises from the distinction between crystallographic
and non-crystallographic maps. A crystallographic map
Ronaldo Alves Pinto Nagem wrote:
Dear CCP4 users,
I was using MAPPROT from CCP4 package to rotate/translate an electron
density map in order to superpose maps from different space group
crystals. However, when applying the same operations (euler angles +
translation OR rotation + translation
See: that is an email address I understand .. sort of ... Is that
especially big or very small (in rms/sigma units)?
Good question. The calculation of the sigma level is local in this case,
and not uniform across the whole map of the world. In Britain, size 44
corresponds to 9.5 sigma
I have had a similar experience.
I was trying to model a bunch of waters to simulate an unknown ligand (UNL) in
an unmodeled density. The waters were all in different alternate conformations
of the same residue number. When the occupancies of these waters were set to
0.5, the vdw repulsion
If sum of occupancies of atoms is less than or equal to one and atoms
are not in the same residue with the same alt code then they do not
see each other. Otherwise they see each other and there is vdw
repulsion between them. this has not changed substantially since the
first version.
On Wed, Jul 30, 2008 at 8:17 AM, Garib Murshudov [EMAIL PROTECTED]wrote:
Dear Snageetha
1) Could you check please if specified atoms have zero occupancy. Atoms
with zero occupancy are considered as absent and there are not restraints on
them
They do not have zero occupancy.
2) symm y at
I am looking at my ligand library file that ProDRG generated. I do not see
any column id that indicates that it is a restraints weight or such. Could
you tell me exactly which one I should edit?
Thanks,
Sangeetha.
On Tue, Jul 29, 2008 at 3:23 PM, Robert Immormino [EMAIL PROTECTED]wrote:
There should be something like:
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
MAN-b-D O1 C1single 1.4100.020
MAN-b-D C2 C1single 1.524
Hi Garib,
This is a side-question. What you just said writing to Abhinav explains
why I have problem of some repulsion between identical ligands with
different tail conformations when I try to refine them at 25% and 25%
occupancy. In my case the overall occupancy of the ligand is not
Hi
While building from scratch in Coot (3A resolution), if I can supply
NCS operators in CCP4 format, is it possible to display NCS related
molecules in the same way as crystallographic symmetry related ones?
External scheme script is fine if that is the way..
(I worked out the operators using
Partha Chakrabarti wrote:
While building from scratch in Coot (3A resolution), if I can supply
NCS operators in CCP4 format, is it possible to display NCS related
molecules in the same way as crystallographic symmetry related ones?
External scheme script is fine if that is the way..
Yes.
If
Hi Michele!
-did you go in steps from 10 to 40 C? did you monitor drifts while doing
that? has the energy range, where you do not observe problems, changed?
In fact I was not planning to do that cause 40ºC
seems to be the monos basal temperature. In addition, I operated
I prefer occupancy that reflects state of things and underlying
chemistry. Then interpretation of the results becomes much better.
VDW repulsion may be a little bit tricky to deal with in complicated
case with the current version (we are adding an option to deal with
coexistence/mutual
Summary:
Problem: I was using MAPPROT from CCP4 package to rotate/translate an
electron density map in order to superpose maps from different space group
crystals. However, when applying the same operations into the maps and
into the pdb files the maps and the pdb files do not superpose. I tried
I am looking at a protein model (no electron density) that has a highly
distorted helix. I would like to idealize this helix in the context of the
protein, e.g. do least squares idealization with restrains on the backbone
torsion angles, with the smallest possible divergence from the initial
Refmac should be able to do this without moving stuff too much. CNS
(no simulated annealing) also can do this kind of thing. If it
becomes problematic, you can restrain the backbone. You can also do
this via coot (which uses refmac I am pretty sure).
William G. Scott
Contact info:
Can try HELANAL
Thanks and Regards
--
ARNAB BHATTACHARJEE
Dept. of Bacteriology and Immunology
SERO Group, Haartman Institute
Haartmaninkatu 3
University of Helsinki
FIN-00014 HELSINKI
Tel. +358-9-191 26385
Fax. +358-9-191 26382
Structural Biology and Biophysics
Macromolecular X-ray
This is way off-topic, but that's never stopped me before. And what
group is better qualified to pontificate about matters lying at the
intersection of computers and optics than this one?
The LCD projector in our departmental seminar room was stolen over
the weekend (!), and I have been
Pat,
Anandtech is a tech website that does alot of hardware reviews on just about
everything you can think of. I don't know what your budget is or what
resolution it is you're looking to project but you can get a 1920x1080
projector anywhere from $9000.00 and up. They may be somewhat pricey,
Hi Phil,
If you have a reasonably recent version of the cctbx around (phenix, cci apps,
maybe ccp4), try
this:
import scitbx.math
rotation_matrix = (1,0,0,0,0,1,0,-1,0)
fm = scitbx.math.r3_rotation_axis_and_angle_from_matrix(r=rotation_matrix)
print fm.axis
print fm.angle(deg=True)
The
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