and struggle is on the peak...
There are a number of ccp4bb postings about crystal reproducibility or crystal
diffraction improvement. Search the archives for these.
F
-
Francis E. Reyes PhD
215 UCB
University of Colorado at Boulder
Graeme and Bob,
Wow... It's great to learn from actual experiences.
Thanks much for this write up.
If this were stackoverflow, +1.
F
On May 8, 2013, at 12:32 AM, Graeme Winter graeme.win...@gmail.com wrote:
A couple of extra comments on top of Bob's rather comprehensive
...@gmail.com
wrote:
I/Isig.=4.4
-
Francis E. Reyes PhD
215 UCB
University of Colorado at Boulder
Ok, I'll bite.
I dare anyone who considers themself an expert macromolecular crystallographer
to find a way to build out of this map.
I put emphasis on this map.
Short of actually cheating (see below), there doesn't seem to be any automated
way to arrive at a solved structure from these
to another).
Thanks for your help,
Nicolas
-
Francis E. Reyes PhD
215 UCB
University of Colorado at Boulder
On Dec 12, 2012, at 2:55 PM, Francis E Reyes wrote:
I've had good experience with GETAX if you have a self rotation peak.
Be careful about moving the NCS operator from program to program.
Phenix/DM/RAVE all have specific formats for how it should be presented.
F
On Dec 12, 2012
-
Francis E. Reyes PhD
215 UCB
University of Colorado at Boulder
Hi Randy
When you say carried along are you saying that they are used as part of the
molecular replacement search? Or are they temporarily put aside and them simply
added to the PDB in frame with the molecular replacement solution (but are not
part of the weighted structure factors output in
[1] In addition to using lower resolution data, you should check a variety of
RMSDs as well. In fact constructing an RMSD / high resolution contour plot
would be beneficial to determine the optimum set of parameters. (That is if
you're using PHASER).
[2] You say you suspect two molecules
crystals have one domain that is the same in each. We'd
like the average the one domain between the crystals, but leave the other
domains unaveraged.
How do we describe that to dmmulti?
thanks,
Dave
--
-
Francis E. Reyes PhD
215 UCB
With DM errors, it would be best to supply the input you used for DM as well as
DM's complete error output.
On Sep 2, 2012, at 9:59 PM, Sofia Caria wrote:
Dear all,
Recently I have been playing with some twinned data (Britton alpha 0.447).
Phasing was done by MR and since I have
Anyone know of a util that'll add hydrogens in a naming scheme consistent with
CNS? (reduce doesn't do this).
Thanks!
F
-
Francis E. Reyes PhD
215 UCB
University of Colorado at Boulder
E. Reyes PhD
215 UCB
University of Colorado at Boulder
of Structural Biology
School of Biological Sciences
University of Auckland
Thomas Building 110
3a Symonds St
Private Bag 92019
Auckland 1142
New Zealand
ph: +64 9 3737599 ext 84155
fx: +64 9 3737414
On 17/07/2012, at 2:53 PM, Francis E Reyes wrote:
The cell predictions look like they're
Do you have crystals?
Do they diffract? If so, to what resolution?
What resolution do you require to answer your biological question?
F
On Jun 12, 2012, at 7:46 PM, LISA science...@gmail.com wrote:
Hi all,
My work is to solve huge complex containing 4 different proteins and total
For the RNA I recommend Eric Westhof's Assemble.
F
On May 23, 2012, at 9:32 AM, jens j birktoft wrote:
Hi everybody,
Does anyone know of a (non-commercial) software that are suitable for
modeling DNA/RNA structures. Coot is great, however I am looking something
that allows more
P21.. You sure about this space group? (very high confidences for space group
and laue group in pointless?)
F
On Apr 19, 2012, at 12:20 AM, LISA wrote:
Hi all,
I am trying to solve one structure by molecular replacement with phaser in
CCP4. This a complex of a multi-domain domains
in this region because of disorder or bad model
phases?
Would love people's thoughts on this one,
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
for most
crystallographic refinement packages).
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
It seems that deposition of map coefficients is a good idea. Does someone have
an mtz2cif that can handle this?
Thanks!
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
I'm now preparing for the flood of 'unsubscribe ccp4bb' requests
On Apr 2, 2012, at 9:15 AM, Bernhard Rupp (Hofkristallrat a.D.) wrote:
Guys,
http://www.youtube.com/watch?v=CobZuaPMQHw
second 9 in this 22 sec video
-Original Message-
From: CCP4 bulletin board
is there?
thanks in advance for help and suggestions..
regards
Shanti Pal Gangwar
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
.
Perhaps a screen shot of one of the images where this is happening would be
helpful. So we can judge the quality of the diffraction / whether the space
group is correct, etc.
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
http://skuld.bmsc.washington.edu/scatter/AS_form.html
Maybe useful to you.
However, I would advise to do a fluorescence scan over the range given in the
graph and then use chooch to provide the precise energies for your peak and
inflection.
If you have a large crystal don't expose all of
data if we consider the difference.
I appreciate your valuable suggestions.
Thanks
Raj
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
in the same drop.
Thanks for any input.
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
of peaks on the self rotation maps).
Any help would be appreciated.
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
). Or the user can go rogue
and 'Ctrl-Click' install any application.
http://www.apple.com/macosx/mountain-lion/security.html
Personally I'll probably choose Mac App Store and identified developers. (I
imagine this will be the default).
-
Francis E
(for free) and then distribute your public key to the community, in case
you want to do something similar.
[FUD] OS X won't trust those keys, only the ones that come from apple [/FUD]
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
Acta Cryst. (1997). D53, 734-737[ doi:10.1107/S0907444997007233 ]
The Ultimate Wavelength for Protein Crystallography?
I. Polikarpov, A. Teplyakov and G. Oliva
http://scripts.iucr.org/cgi-bin/paper?gr0657
may give some insights.
To the OP, have you solved the structure? In some cases,
not a surprise to me and if you have not tried small
crystals from the same batch well then you missed 50% of your chances to
solve s structure with the first light the crystals saw.
Jürgen
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
crystals diffract? Do you see the analogue?
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
.
Any suggestions to improve diffraction would be welcome.
Thanking you in advance.
Theresa
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
in Crystallography and Biophysics
University of Madras
Chennai,India
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
atoms for each )
were used in phasing. Aren't analyzing the differences (independent of
source) the important bit anyway?
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
at home. If it kills your crystals, move to more toxic things...
Thanks in advance,
Federica
Cheers,
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
- I'll have to check out the details of
how phenix handles it, and give it a try.
Pete
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
/events/CCP4_2012/programme.html . All details
are accessible from the ccp4 homepage (http://www.ccp4.ac.uk).
Charles Ballard
CCP4
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
On the other hand, shooting a lower resolution crystal may get you the
conformation of the disordered domain.
Surprising at first thought, but was true in p97/VCP from the Brunger Lab.
F
On Dec 7, 2011, at 11:47 PM, atul kumar wrote:
Dear all
I have crytals which diffract up to
to set drops, only DNA crystals. Kindly suggest me, what could be done.
Thanks Regards,
Umar Farook.S
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
is different. I could
test my hypothesis by reprocessing the data were it available.
and thank you for providing yours .
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
for improvement of a group
II intron structure. Acta Crystallogr D Biol Crystallogr (2010) vol. 66 (Pt 9)
pp. 988-1000
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
sure this has to be done, but consensus
in this area is equally important.
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
at similar features in both maps and using lsqkab to get the transformation
matrix; but this approach would probably need tuning to get a good alignment.
Good luck,
Pete
Francis E Reyes wrote:
Hi all
I'm using dmmulti and one of my crystal forms seems to have a better solvent
mask (after
).
Is there some formatting error I'm not seeing?
Thanks!
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
algorithm by those programs during integration, or is it up to
the scaling/merging (by SCALA for example) step to deal with them?
Thanks!
F
inline: PastedGraphic-1.tiff
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
density maps.
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
I already started with an ellipse... should I extend with a rectangle down the
shaft of the beamstop?(this is FRAME.cbf after integration)
inline: PastedGraphic-2.tiff
Thanks!
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado
Scott wrote:
she asked were a few questions about a specific computer (HP Z210 8 GB with
a low end Quadro Nvidia 400 512 MB) running any Linux, and a specific
computer (IMAC 4 GB 2.5 GHz with AMD Radeon HD 6750M 512 MB)
-
Francis E. Reyes M.Sc
better than then drives from 2007. I doubt it though.
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
you want to use it as a tool
to verify the location of a ligand binding site.
Thanks!
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
specific to my setup?
Cheers,
Ed.
--
After much deep and profound brain things inside my head,
I have decided to thank you for bringing peace to our home.
Julian, King of Lemurs
-
Francis E. Reyes M.Sc.
215
residue names, however pdb may use
only one of them.
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
body or very restrained (
secondary structure | reference structure | etc ) refinement of the coordinates
for helping the fit.
Thanks!
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
this and subsequent refinement still does not produce the
expected density for the chains.
or
[3] Your solution here.
If this situation has been discussed before, please let me know .
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
are not compatible. I'm trying to build an RNA
molecule by the way.
Any suggestions?
Eric
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
at the Ir peak and Ir at the Co peak. Use both to cross validate your model
(when you get to it) and calculate experimental phases using both (dual SAD or
2wl MAD for each heavy atom).
So no it's not surprising.
F
-
Francis E. Reyes M.Sc.
215 UCB
to scale) ?
Am I interpreting this correctly?
Thanks!
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
them to be black on the
walls. I'm looking for a supplier / catalog number of such plates.
To save bb spam, I'll take replies privately.
Thanks!
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
Never had problems with evaporation (and this is in the relatively dry
climate of Denver, CO, especially in the winter when the relative
humidity is in the low 20%).
Using the Thermo Scientific Nanodrop 2000c.
We use it also as a prerequisite for ITC, which can be very sensitive
to proper
of the data is about 3.1A).
The unit cell is:
142.0500 142.0500 137.9200 90. 90. 120.
P6422.
Any ideas appreciated,
Thanks!
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
Can someone return their full path of the location of multilog (used
for browsing dmmulti output)?
I can't find it in my ccp4-6.1.13 installed from Mr Scott's distrib.
Thanks!
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
position with respect to your protein.
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
I doing wrong? Please help me with
suggestions
Many thanks
Careina
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
that explains
how 'Scor' is computed?
[2] Based on the results above, it seems that P 21 21 21 is the
correct s.g.?
[3] Why the failure?
Thanks!
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu
Hi all
Is there a walkthru/tutorial for processing inverse beam images with
imosflm/scala? Googling a few things didn't get me anywhere.
Thanks!
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu
. Our apologies for the
inconvenience.
Best wishes,
Ronan
Ronan Keegan
CCP4 Group
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
it with water refines perfectly with
no indication of positive difference density even at 2.0 sigma cut
off. Should I modelled this density as water or as Mg2+. Your
opinions are appreciated.
JL
test.png.odp
-
Francis E. Reyes M.Sc.
215 UCB
University
Zernike Institute for Advanced Materials
University of Groningen
Nijenborgh 4, 9747 AG
Groningen, The Netherlands
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC
-
-0.1051 -0.9808 0.1642
shift -
invert -
-108.0451 47.655 -17.5654
end
Can someone supply me with the correct matrix to input into DM (and
what convention it is?)
Thanks
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg
Oops
It pays to view the pdbset log as it gives the right matrix.
F
On Dec 1, 2010, at 10:41 AM, Francis E Reyes wrote:
Hi all
I'm trying to figure out rotation matricies for ncs averaging in DM.
Except the conventions have got me confused.
The following input script for pdbset
CCP4'ers,
Are 9 datasets the maximum for an mtz file? or a single run of cad?
The manual (http://www.ccp4.ac.uk/html/cad.html) seems to suggest that
9 is the limit per cad run but not for a given mtz.
F
-
Francis E. Reyes M.Sc.
215 UCB
Hi all
Are there any online/offline 3D crystal lattice builders to explore
symmetry relationships in the unit cell given say a space group and
unit cell parameters? I need one for an educational opportunity.
Thanks!
F
-
Francis E. Reyes M.Sc
one backsoaked.
Thanks
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
, alpha=119, beta=119, gamma=90),
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Hi all
I'm interested in the scenario where crystals were screened at home
and gave lousy (say 8-10A) but when illuminated with synchrotron
radiation gave reasonable diffraction ( 3A) ? Why the discrepancy?
Thanks
F
-
Francis E. Reyes M.Sc
never are able to completely get rid of Y. How does this affect the
analysis of determining the derivative's affinity by ITC?
References or personal experience is appreciated!
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg
to be able to accommodate 35 cm (wide) by 26-30cm (height) plates.
Please reply privately.
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Sorry a late comer to this thread but the OP mentioned tweaking the
error model in HKL2000. I have heard this before.What's the validity
in this? Does it actually help or does it only help the integration
numbers but you'll pay for it during refinement?
FR
On Jun 23, 2010, at 8:25 AM,
Hi all
I've been playing around with charge flipping for macromolecular
substructure determination with pretty promising results. I'm
particularly attracted to the fact that it solves structures in P1,
with no space group assumptions and curious how it would handle some
of the
Hi all
I'd like to add a phase error to my PHIB's and FOM's (experimental phases) that
increases linearly with higher resolution.. it's akin to taking good phases and
making them bad. Any approaches on how this can be done?
Thanks
FR
-
Francis Reyes
Hi all
I have a solved structure that crystallizes as a trimer to a reasonable
R/Rfree, but I'm trying to rationalize the peaks in my self rotation. The space
group is P212121, calculating my self rotations from 50-3A, integration radius
of 22 (the radius of my molecule is about 44). I can see
Is this a cause for concern? FOM's are over 0.5 and Phasing Power is over 2.0.
Thanks
FR
-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA
Hi all
I'm in search of literature *detailing* low resolution [4-5A] phasing
protocols. Heck I'll take detailed thesis chapters (since they tend to be more
detailed than pubs anyway). If you ribosome people are on this board I'd love
to hear from you.
[sarcasm]Searching for 'grasping at
Hi All
I'm having trouble with the following ...
title [No title given]
operator -1/2*h+1/2*k-l, 1/2*h-1/2*k-l, -1/2*h-1/2*k
labin I(+)=I_Unspecified(+) SIGI(+)=SIGI_Unspecified(+)
I(-)=I_Unspecified(-) SIGI(-)=SIGI_Unspecified(-)
end
I keep getting symmetry operator error.
Thanks
FR
How does one calculate a simulated annealing omit map in cases of non
crystallographic symmetry? The omit map is being used to identify the
presence and configuration of a ligand and surrounding residues. The
omit region therefore will contain the ligand and residues within
hydrogen
Or know of any references besides Declercq and Evrard, 2001 ? I'd love
to hear from you. Please PM me.
Cheers
FR
-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640
+1 phenix FTW
FR
On Jan 13, 2010, at 3:28 PM, Peter Zwart phzw...@lbl.gov wrote:
try using
phenix.reflection_file_converter data.sca
--change_of_basis=h,-k,-h-l --sca=reindex.sca
or something like that
HTH
Peter
2010/1/13 Francis E Reyes francis.re...@colorado.edu:
Hi all
I have
What is the space group? Is there unmodeled density? Are all residues
in your construct built? What is the refinement protocol?
FR
On Dec 18, 2009, at 6:47 AM, james09 pruza james09x...@gmail.com
wrote:
Dear All,
I am trying to solve a 2.55 A resolution data set. The R-factor is
Hi all
I have a rotation + translation component for the 2-fold given to me
by GETAX using low resolution low quality experimental maps. I
understand that these are input into DM for NCS averaging. What are
signs of progress as well as how does one usually optimize the mask?
When doing
Hi All
I'm interested in screening small molecule libraries against my xtal
for potential binders. There are many papers that cover this (http://www.nature.com/nbt/journal/v18/n10/abs/nbt1000_1105.html
, for example).
If you have had experience in this field, please email me privately as
Hi all
I have pretty low res data (4-4.5A) and was wondering what's the
suggestion for allowing the bfactors to vary or keep them fixed during
scaling. If I fix them, xtriage reports wonderful anomalous signal
whereas if they are varied, the anomalous signal is gone. I have
natives and
Hi All
I have a predetermined matrix from labelit, how can I use it with
imosflm? I add the matrix file under 'Images', but I cannot integrate.
Thanks
FR
-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver
Hi all
Can XDS take in additional images that have a different template name and
reside
in a different directory? The reason is that I have high res images and then
low res
images in different directories that I want XDS to consider.
Thanks!
FR
Hi all
I'm working on a structure of an RNA. Phases were obtained via SAD and
the structure was refined to 21/26 % on R and R-free with a resolution
of 2.8A, single molecule in the ASU. 7 residues were missing in a
disordered loop out of a total of 54 residues in the asu. The cell was
Hi all
I'm looking for anyone who has had (practical) experience using SAXS
data to phase 4.2 A crystals. Please email me.
FR
-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2
Hi all
I'm trying SIR on my crystal both are C222.
Native
Cell Dimensions: 97.66 243.45 87.62 90 90 90
Resolution: 4.3
Derivative
Cell Dimensions: 96.9100 244.66 87.61 90 90 90
Resolution: 4.7
. I plan to scale together using FHScal. Ctruncate says that my
derivative has strong
Hi All
Im receiving some strange patterns in my pattersons. Space group is
C222 with no confidence (due to resolution) of systematic absences to
transform to C2221.
Thanks!
FR
pattersonmap.pdf
Description: Adobe PDF document
-
Francis Reyes
For a given reflection (h,k,l) how much does each situation increase
the redundancy ? and which maximizes the ability to measure anomalous
differences? (so assume we're separating friedel pairs here)
a) measuring the same reflection again
b) measuring a symmetry related reflection
c) both
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