Dear all,
I've written
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/INTEGRATE
hoping that this will explain how XDS works (the last part focuses on
the overlap question). Caveat: this is written to the best of my knowledge.
I would also like to draw your attention to the article
Hi,
While on the subject, a related matter that may be of relevance:
surprisingly many people do not remove the outliers after XDS
processing (via using the REMOVE.HKL file) and this, in certain
cases, has its effects on the intensity distribution and 'refinability'.
Petri
On Feb 21, 200
There is of course nothing stopping you from having both severe
overlap problems and twinning :-(
In this case, XDS-processed data is clearly twinned, if one were to
believe moments and the cumulative intensity distribution calculated
by truncate (and everyone should - channelling Dr. Dodso
On 21 Feb 2008, at 19:11, William Scott wrote:
"Then I used CNS to do annealing, then use refmac to do rigid body
refinement."
That can be why the R-factors went up. Rigid-body subsequent to
simulated
annealing will (if anything) undo the refinement ...
...just wondering...
I guess you ke
Most reagents that modify side chains are also (not surprisingly) toxic.
Many of them are small and therefore membrane-permeable.
Look up recent works on in vivo 'click chemistry'. Unfortunately I doubt
that these compounds can be classified as 'cheap'.
If you want to do this in vivo, you're pro
Hi Simon,
When data are processed with XDS and converted to an mtz file by the route you
suggest unmeasured reflections will simply be absent from the mtz file rather
than denoted by a missing number flag. Prior to missing number flags (back in
CCP4 3.something) it was common practice to leav
Hi,
You can use dimethylamine borane (DMAB) for reductive methylation of the
surface exposed K's. You may also try NaBH4 or sodium cyanoborohydride but the
first may be best.
Don't know about D's and E's.
Best,
Debanu.
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTE
Dear Crystallographers,
I am looking for a way to modify any specific set of sidechains in my
protein (e.g., all K's, or all D's and E's, etc.). A few requirements:
1. Relatively cheap
2. Definitely non-cell-membrane-crossing
3. Specific
4. Any reasonable amount of change in mass (+ 5-5000 Da?
That was _supposed_ to say "I'm not sure ..." !
On 21 Feb 2008, at 21:01, Phil Evans wrote:
On 21 Feb 2008, at 18:24, George M. Sheldrick wrote:
All SHELX programs and XPREP are also indifferent to the asu choice
and to whether the data have been merged or not (even SHELX-76). It
is CCP4 h
On 21 Feb 2008, at 18:24, George M. Sheldrick wrote:
All SHELX programs and XPREP are also indifferent to the asu choice
and to whether the data have been merged or not (even SHELX-76). It
is CCP4 historical baggage and high time it was eliminated.
I'm sure that many if any of the CCP4 progra
Hi,
Was this an install from executables, or from source?
I have just installed Ubuntu Gutsy on my laptop (everything including
wireless worked out of the box - I think Ubuntu is great for people who
want to simply use computers).
I installed CCP4 6.0.2 with the automatic installer from the
In this case, XDS-processed data is clearly twinned, if one were to
believe moments and the cumulative intensity distribution calculated
by truncate (and everyone should - channelling Dr. Dodson).
Why I'm worried about XDS separating relatively overlapped spots is
the funny intensity stats
Dale Tronrud wrote:
In summary, this argument depends on two assertions that you can
argue with me about:
1) When a parameter is being used to fit the signal it was designed
for, the resulting model develops predictive power and can lower
both the working and free R. When a signal is per
re: possible solutions for those troobleshooting ccp4 and ccp4i.
On Ubuntu 7.10 - Gusty:
A necessary shared lib file for ccp4 6.0.2 called libblas.so.2 was
not present on my fresh system. So provide a link to libblas.so.3.0
On any system:
Perhaps all your new jobs in ccp4i report a job statu
"Then I used CNS to do annealing, then use refmac to do rigid body
refinement."
That can be why the R-factors went up. Rigid-body subsequent to simulated
annealing will (if anything) undo the refinement ...
Anastassis Perrakis wrote:
> Just to point out that I have missed the NCS presence; Liju
Just to point out that I have missed the NCS presence; Lijun is
*perfectly* correct; even more I should emphasize the point and
say that at 3.0 A, Thou Must Use NCS (if I say again anything about
Gospels and Kleywegt we end up with more facebook groups ...)
I think there is no reason at this
Yang Li,
I personally always take this kind of thing as "instability" in
refinement. Your independent reflection numbers might be much less
than the to-be-refined parameters, and still you sacrificed some for
R-free calculation. I think there is no reason at this resolution
edge (~3A),
All SHELX programs and XPREP are also indifferent to the asu choice
and to whether the data have been merged or not (even SHELX-76). It
is CCP4 historical baggage and high time it was eliminated.
On the official thread of this discussion, my impression is that 3D
integration programs (like XDS)
I should add that inspecting the average three-dimensional profiles in
INTEGRATE.LP could give you an indication if you have overlaps or not.
The profiles look like slices through a 3D unimodal gaussian. If you
have overlaps it will be revealed by bi-/multi-modal features. However,
these are avera
Dear James --
I have a tough ~3.5 Å (pushing it) MR problem where I have a
solution of sorts, but because I'm working with a heterodimer of
two closely related subunits (with two such heterodimers in the
ASU) I have a 2**2 possibilities for the arrangement of these
subunits in the ASU. Ea
Hi,
Going back to your original question regarding integration with XDS.
On Feb 20, 2008, at 11:54 PM, Engin Ozkan wrote:
I have been recently relying on XDS quite a bit, but at the same
time worrying about how XDS treats overlaps. We had one dataset
that both HKL2000 and Mosflm would show
I pretty much agree with Tassos, but he neglected to mention that on an
Intel Mac you can also run Linux and Windows at native speeds, on the
same machine, simultaneously. With Parallels software, you also get the
added advantage of OpenGL 3D hardware acceleration, whereas with VMWare,
you get 64
doh... of course I also run CAD - which means (according to
XDSCONV.LP) that the data would have already been converted into the
CCP4-asymmetric unit prior to me getting to DATAMAN to pick my Rfree
set.
In which case we have solved the reciprocal asymmetric unit problem
and thus get back
or use phenix, which is indifferent to format and asu choice.
P
2008/2/21, Michele Lunelli <[EMAIL PROTECTED]>:
> Simon Kolstoe wrote:
>
> > I converted the resulting
> > XDS_ASCII.HKL using xdsconv and then f2mtz ready for phaser and refmac.
> >
>
>
> Sorry if this is obvious, but you shou
Hi all,
To respond to a users suggestion, I've added drag-and-drop boxes to the crystal
screen wizard, so now you can now set up your screening conditions in any order
you want (web 2.0-ified if you will). You can also mix and match different kits
from different manufacturers in the same tray.
Hey there,
just want to give a quick update on my dials project. You might
remember the question regarding the OSX drivers and USB-to-serial adaptor.
Well, the driver on Dave Gohara's site (http://smackfumaster.com) does
its job with the Digitus adaptor I have
(http://www.digitus.info/scrip
Simon Kolstoe wrote:
I converted the resulting
XDS_ASCII.HKL using xdsconv and then f2mtz ready for phaser and refmac.
Sorry if this is obvious, but you should also run CAD after f2mtz, as reported
at the end of the log file XDSCONV.LP.
Michele
In the past I have used the USF program DATAMAN to pick my Rfree in
thin shells. Thus my data goes XDS-> XDSCONV-> DATAMAN-> F2MTZ in
order to get a reflection file that refmac and phaser are happy with.
Do I then need to run the UNIQUEIFY script selecting the option "keep
existing FreeR da
On 21 Feb, Kay Diederichs wrote:
> In the case of a new project, one should run "uniqueify" or some other
> means of assigning reflections to the free set (thin shells come to
> mind; see earlier discussions on CCP4BB).
As I said in a previous posting, a better solution would be to take a
ran
Hi all,
just to second previous statements: Phaser has done wonders for me in a few
tough cases, also at low resolution: Eg. various 6-10AA data sets with
highly homologous search models. Or a rather bad search model: 1.8AA rmsd
over ~50% of the residues. Often up to a point where the solution was
I use XDSCONV to make the mtz file using all of the reflections. Then I
use uniqueify in CCP4 to make sure the asymmetric unit is correct for
CCP4, and tag the test set.
Bernie Santarsiero
On Thu, February 21, 2008 9:32 am, Dirk Kostrewa wrote:
> Usually, I run CAD first after F2MTZ to make sure
Usually, I run CAD first after F2MTZ to make sure that the
reflections are in the correct reciprocal asymmetric unit for CCP4
programs. I think, UNIQUE on its own doesn't do this, but the
UNIQUEIFY script calls CAD, UNIQUE and FREERFLAG for setting a
FreeR_flag column. The latter may or may
The only other comment that I'd add is XDS builds real three-dimensional
profiles, whereas HKL2000 uses two-dimensional profiles. Thus, you can
imagine that if you have already defined a 3D profile, XDS only needs part
of the reflection, over one or more images, to estimate the overall
intensity of
In my experience when going from XDS via some intermediate file to mtz format,
XDS uses in some cases a different reciprocal asymmetric unit as mtz uses,
which may result in only half of the reflections being used and/or ccp4
programs getting confused. By using UNIQUE, one makes sure that the re
Simon Kolstoe schrieb:
Whilst we are on the subject of XDS...
I had difficulty processing a data-set in mosflm the other day so on the
recommendation of a colleague switched to xds which, with a bit of
tweaking, seemed to work really well. I converted the resulting
XDS_ASCII.HKL using xdsconv
James Stroud wrote:
Hello All,
I have a tough ~3.5 Å (pushing it) MR problem where I have a solution
of sorts, but because I'm working with a heterodimer of two closely
related subunits (with two such heterodimers in the ASU) I have a 2**2
possibilities for the arrangement of these subunits in t
Whilst we are on the subject of XDS...
I had difficulty processing a data-set in mosflm the other day so on
the recommendation of a colleague switched to xds which, with a bit of
tweaking, seemed to work really well. I converted the resulting
XDS_ASCII.HKL using xdsconv and then f2mtz ready
Absolutely try Phaser!
See Phaser documents for all the nifty combinations. Multiple molecules in MR
model; break down
molecule by domains etc etc. You can trim down side chains, make hybrid models
and what not. All
easy to get up and going through the GUI. Once the GUI drove me insane because
Dear Flip,
I have had trouble with video drivers for various flavours
of Linux. If if driver is not working then, as you say, you just
cannot do anything after booting normally. You need to boot the
machine in a safe mode or single user mode (init 1). You can then
edit the /etc/X11/XF86Config f
What virtualisation software are you using?
VMWare, virtualbox, xen?
Not seeing anything means, you can't even see to prompt when the virtual
machines tries to boot from CD/DVD?
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Thu,
This actually pops up a question on a somewhat related issue, I've recently
tried to install Fedora 8 on a virtual PC, but I get caught up with the
video display being completely warped. Since I don't see anything I cannot
even begin to troubleshoot the issue. Has anybody got a solution for this?
Hello All,
I have a tough ~3.5 Å (pushing it) MR problem where I have a solution
of sorts, but because I'm working with a heterodimer of two closely
related subunits (with two such heterodimers in the ASU) I have a 2**2
possibilities for the arrangement of these subunits in the ASU. Each
Dear Yang Li,
On Feb 21, 2008, at 8:23, yang li wrote:
Dear All,
I have a 3A structure, the quality of the data is not very good.
I will stick a bit on your opening statement.
Having 3.0 A data is sometimes a fact of life - most unfortunately.
Sometimes, you simply cant do better with
Aurigene is looking for young, energetic and committed individuals to
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Engin Ozkan schrieb:
Hi everyone,
I have been recently relying on XDS quite a bit, but at the same time
worrying about how XDS treats overlaps. We had one dataset that both
HKL2000 and Mosflm would show to have severe overlaps, as expected due
to unit cell parameters and the unfortunate crys
Dear all,
A 4-year post-doctoral position to study pattern recognition receptors
of the innate immune system is available in the protein crystallography
group of Piet Gros and Eric Huizinga at Utrecht University.
Details of the project and information on how to apply can be found at:
http://ww
Ok, I downloaded and installed CCP4 from the website on Jan 24, left the
defaults as they were.
Flip
-Original Message-
From: Scott Pegan [mailto:[EMAIL PROTECTED]
Sent: Wednesday, February 20, 2008 22:49
To: [EMAIL PROTECTED]
Cc: ccp4bb@jiscmail.ac.uk
Subject: Re: [ccp4bb] Vista
My att
Deena,
A lot of this comes down to personal preference at the end of the
day..you just have to find what works for you.
I primarily use MacOSX and Linux. I also have a Vista partition on my
laptop to share Microsoft office files with others in the department
that use Windows or Macs..no comm
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