On Sep 29, 2011, at 2:48 AM, Nat Echols wrote:
I don't know of any macromolecular crystallography programs that don't run on
Mac -
Hey there,
does this mean that SHARP works on a Mac?
ciao,
s
--
Sebastiano Pasqualato, PhD
Crystallography Unit
IFOM-IEO Campus
Cogentech - Consortium for
Yes, SHARP and BUSTER both work on a Mac.
Cheers,
Dirk.
Am 29.09.11 09:45, schrieb Sebastiano Pasqualato:
On Sep 29, 2011, at 2:48 AM, Nat Echols wrote:
I don't know of any macromolecular crystallography programs that
don't run on Mac -
Hey there,
does this mean that SHARP works on a Mac?
Thanks Dirk,
that's good news.
I'll take a look at it, then.
thanks,
ciao,
s
On Sep 29, 2011, at 9:51 AM, Dirk Kostrewa wrote:
Yes, SHARP and BUSTER both work on a Mac.
Cheers,
Dirk.
Am 29.09.11 09:45, schrieb Sebastiano Pasqualato:
On Sep 29, 2011, at 2:48 AM, Nat Echols wrote:
Dear All,
Apologies for bit off-topic. I am in process of purifying a protein by
ion-exchange (cation)
using 0.5-3M NaCl gradient. And I get a sharp peak which is western
positive. Following elution,
I wash the column 10 column volume with 3M NaCl. and now when I
wash the column
with water, I
I am routinely having the Mac vs Linux conversation with crystallographers and
new students, especially given the price of Macs.
Generally I think that the extra money spent on a Mac pays for less time spent
messing around installing software, sorting out dependencies, swearing at the
less
Hi Sebastiano,
On Thu, Sep 29, 2011 at 09:52:44AM +0200, Sebastiano Pasqualato wrote:
does this mean that SHARP works on a Mac?
yes (since 2004), same for BUSTER (since 2009) and autoPROC.
Cheers
Clemens
--
***
* Clemens
This discussion will rage forever, it seems, but that won't stop us
all chipping in. My experience is the opposite: all crystallographic
software I use is available as binaries for the major linux distros,
and installs without problems. Ubuntu is easy to maintain on desktops
(your mileage on
Le 29/09/2011 11:43, Johan Turkenburg a écrit :
This discussion will rage forever, it seems, but that won't stop us
all chipping in. My experience is the opposite: all crystallographic
software I use is available as binaries for the major linux distros,
and installs without problems. Ubuntu is
Since water is unbuffered, you are likely changing the pH of the solvent,
desorbing additional protein. If you are working unbuffered, your IEX
results will be unpredictable.
Roger Rowlett
On Sep 29, 2011 4:55 AM, K Singh ksc...@gmail.com wrote:
Dear All,
Apologies for bit off-topic. I am in
2011/9/29 Simon Kolstoe s.kols...@ucl.ac.uk:
Generally I think that the extra money spent on a Mac pays for less time
spent messing around
installing software, sorting out dependencies, swearing at the less than
effective office software etc.
that plagues Linux which is more of a computer
After I ran DETWIN with the estimated 0.46 alpha, my completeness for the
detwinned data is now down to 54%!!!
Is this normal behavior? (I am guessing yes since the lower symmetry untwinned
dat is P1 21 1)
Why do you detwin? It would not be normal procedure if you have twinning.
Molecular replacement programs usually do not have much problem with twinned
data and refinement programs can deal with them more or less properly.
when you detwin then errors are increased (As far as I remember
Yuri,
Detwinning relies on having both twin-related reflections present to
calculate either/both of the the de-twinned data values. Therefore it
magnifies incompleteness depending on where your missing data is with
respect to the twin operator.
I'd recommend against trying to do this with
I am refining in phenix twin law h,-k,-h-l.
Without twinning I was around 0.36 Rfree and 0.25 with twinning.
I am noticing however that my Rgap keeps increasing slowly... (little
concerned now its at 8% - 0.18-0.26 - to 2.4A)
Maps look decent for 2.4A I have a lot of clashes however some are
Simon Kolstoe wrote:
Meanwhile I think windows is slowly improving as a crystallography
platform - and Microsoft is perhaps no longer hated in principle - however
the one student in our lab who opted to go the windows route seems very
limited in the software he can run.
I have a feeling
I am now realizing that! I have been refining with twin law
enabled, its been somewhat succesful.
I have been using phenix and now
getting ready to try refmac...
regards
On Thu, 29 Sep 2011 15:23:13
+0100, Garib N Murshudov wrote:
Why do you detwin? It would not be
normal procedure if
Could be of importance to those who have to use the Lyon or Grenoble
airports (to ship in or out), check out the update from Sept. 27, 2011.
http://www.ill.eu/users/user-guide/safety/important-instructions-for-biological-samples/
Fred.
http://www.ill.eu/
Dear users,
I was trying to process a C2221 data in two different versions
of imosflm (7.0.4 and 7.0.7) using same set of frames, later on
scaled using scala in ccp4 6.1.2. But for m surprise the statistics
were quite different in two cases:
In case of 7.0.4:
Hi
We improved the code between the two versions - i.e. we made
changes that should make processing more reliable. In particular, we
changed the way the different parts of partial reflections are
apportioned in the postrefinement, which was intended to make the
refinement of the
There's one piece of software that does not run on a Mac.
GRAPHent
I tried some years ago to port it to a Mac without success, that's the only
reason I have a dead PC (*technically it has Windows on it but I call it dead
as long as no linux is installed) in my office waiting to get some flavor
I do all my program development on Linux and never liked Windows. However
I recently attended two small-molecule crystallographic workshops where
the large majority of the participants used exclusively Windows, and the
ones who didn't use Windows used mostly Macs. I think the decisive
advantage of
Hi,
I have been extremely happy with the latest Ubuntu release, on both a
Toshiba tablet (the touch screen worked right out of the box) and on a
desktop with the proprietary NVIDIA driver. I haven't had to update,
so I don't know what happens with the NVIDIA driver in that case, but
I can tell
On Thursday, September 29, 2011 12:55:43 pm George M. Sheldrick wrote:
I do all my program development on Linux and never liked Windows. However
I recently attended two small-molecule crystallographic workshops where
the large majority of the participants used exclusively Windows, and the
ones
Hi every one
I have a problem with docking my ligand into the electron density map and make
the connections ( bonds ) with the protein.
It is a Lysine residue that makes a Schiff Base with a long chain aldehyde.
I do not know how to make the bonds and control the torsion angles of the
ligand.
after 1 round of refmac rigid body and restrained refinement with twin law
(estimated alpha 0.47)
I am looking at 0.25 -0.29 Rwork Rfree and overall FOM 0.72.
I also defined NCS restraints...
Yuri,
note, the R-factors in case of twinning are not directly comparable.
Pavel
On Thu, Sep 29, 2011 at 7:25 PM, Yuri Pompeu yuri.pom...@ufl.edu wrote:
after 1 round of refmac rigid body and restrained refinement with twin law
(estimated alpha 0.47)
I am looking at 0.25 -0.29 Rwork Rfree
Hello Sam,
if the ligand dictionary file is not available from the CCP4 monomer library
(refmac would stop when it recognized an unknown ligand), you have to
generate it from either the PRODRG server (
http://davapc1.bioch.dundee.ac.uk/prodrg/) or PHENIX eLBOW (
Dear all,
I just notified that there is a big difference between the Ramachandran plot
analysis results produced by Coot and Morprobity (or Phenix). For the structure
I am working now, Phenix(Morprobity) gives out Ramachandran outliers 0.2%,
favored 95.2%, whileas Coot gives out Outliers
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