Hi Tim:
Thanks a lot for suggeting "exec" in my shell script. It really works
under both shell and PBS; however, the running was just terminated right
after "exec ${DIR}/lx_mapman" was excutated. I am not sure why this
happens:-(
Hailiang
> Hello Hailiang,
>
> On Wed, Jun 23, 2010 at 10:01:04PM
Hello Hailiang,
On Wed, Jun 23, 2010 at 10:01:04PM -0400, Hailiang Zhang wrote:
> Hi there:
>
> I downloaded the binary files of UPPSALA-mapman and they run smoothly
> under linux. However, when I write it into a shell script and run under
> PBS queue, it cannot be excuated. A simple test turned
Hi there:
I downloaded the binary files of UPPSALA-mapman and they run smoothly
under linux. However, when I write it into a shell script and run under
PBS queue, it cannot be excuated. A simple test turned out to be:
(1)
***
[Linux] ./lx_mapman ->works
(2)
***
[Linux]source ${ABSDI
Since no one has answered the SHELX part of this question I'll
jump in. The PRODRG restraints should work as is, assuming you've
named the peptide atoms correctly (C, O, CA, N). But just in case
they don't you can explicitly attach it to the main chain with the
addition of a couple of spare res
I think you should be able to specify two different "NCSR" lines, one to
cover chains A&A' and C&C', and another to cover chains B&B'.
On 06/23/10 18:51, Oganesyan, Vaheh wrote:
Dear bb contributors,
I would like to refer to your expertise and get advice regarding
multiple NCS relations betwe
Dear bb contributors,
I would like to refer to your expertise and get advice regarding
multiple NCS relations between two macromolecular complexes in asu.
Resolution 2.5A, s.g. C2221, R-merge 6%, synchrotron data, 2 complexes
per a.s.u. Each complex consist of three polypeptide chains, let's say
Thank you Tim and Partha,
The reason I do not have clear density of my ligands ( at 1.15 Angs) is that
I have a native-active enzyme complexed with substrate and product forming
at the active site. We have reason to believe from our enzyme kinetics data
that we would be able to capture both the sta
Dear all who answered,
the combination of
- compiling cctbx from source
- modifying the pymol startup script to source the cctbx setpaths.sh AND use
cctbx.python (instead of /usr/bin/python) eventually works.
Thanks to all the responses to make this work.
Tim
On Wed, Jun 23, 2010 at 01:02:03
On Wed, 23 Jun 2010 09:07:36 -0400 "Schubert, Carsten [PRDUS]"
wrote:
> Tim,
>
> I'm shooting from the hip here, but I think the problem is that cctbx
> comes with its own python, which you would need to run both pymol and
> numpy under. According to Ralf it is at least not trivial to utilize th
On Wed, Jun 23, 2010 at 8:21 AM, Graeme Winter wrote:
> There will be a cctbx.python dispatcher now which should set
> everything up - however if you source setpaths_debug I think this
> should make for a happy python as it includes everything from the
> dispatcher.
>
Don't use setpaths_debug -
On 23/06/10 14:40, Fatima wrote:
Dear all,
I'm finishing a refinement using SHELX and Coot (1.3A) and I have a modified
Arginine. There’s a blob of positive density (9.04 and 7.01 sigma) binding NH2
in the 2 conformations. I think it could be a hydroxyl there.
1) How can I add that in Coot?
Hi Tim,
There will be a cctbx.python dispatcher now which should set
everything up - however if you source setpaths_debug I think this
should make for a happy python as it includes everything from the
dispatcher.
At least, that was my understanding.
best wishes,
Graeme
On 23 June 2010 16:17, T
Ok, I just did that.
After sourcing setpaths.sh, PYTHONHOME is set to /path/to/cctbx_build
When I start python and enter
from cctbx import sgtbx
I get an error message about a missing __init__.py
The whole cctbx_build does not contain a single __init__.py\*, but there are
plenty in ../cctbx_sour
Dear Colleagues,
I hope the following detailed review will be of help both with terminology
as well as case studies of a wide variety of kinds, including possible
approaches for moving forward, regarding the various manifestations of
twinning, lattice disorders and multiple crystals.
Best wishes,
J
Thankyou Tassos, Kay and others for the congratulations. Maybe I should
put it in perspective:
Most of the people citing SHELX were small molecule crystallographers,
who do not feel obliged to cite the programs they used only in the
supplementary material.
If you want to be cited you have to w
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, "Zh
Dear Tim,
There are instructions on how to build cctbx against your system
Python (which I assume is the one used by PyMol) here:
http://cctbx.sourceforge.net/current/installation.html#manually-building-from-sources-under-unix
>From there you can also install other Python modules e.g. Numpy in t
Hi All,
The problem has also been solved with a new 2.0A dataset collected over the
last weekend. Same space group and dimensions, much less radiation damage. This
time I used APS SER-CAT's weaker BM beamline.
Thanks,
Tongqing
Tongqing Zhou, Ph.D.
Staff Scientist
Structural Biology Section
V
Dear Carsten,
thank you for the instruction. The cctbx package seems to lack tkinter which is
required by pymol (and maybe numpy, too). How do I install a specific python
module (package? what's the correct term?) 'under' cctbx.python?
Cheers, Tim
On Wed, Jun 23, 2010 at 09:07:36AM -0400, Schube
Dear All,
The problem solved.
I have to remove one of the Dell factory partitions to install Linux. Here is
what I did
1. Shrink the hard drive with Win 7 to give free space for Linux
2. Delete the READER partition (Did not touch the Dell Utility, OS and Recovery
partitions)
3. Install from DVD
The Panne laboratory at the EMBL seeks to recruit an outstanding postdoctoral
scientist in structural biology. Our research focus is directed towards the
structure of macromolecular assemblies involved in the innate immune system and
in epigenetic gene regulation (Panne et al., Cell 2007; Panne,
Actually it probably would be better ask the supplier of your screen
first how they got PEG 1K diluted to 12.5%. If they did hit it then you
have to do the same. But even better idea is to order that PEG 1K from
the same company that sells the screens. It will insure identical
treatment.
My 2 c
When the ACA meeting was in Hawaii (2006?), there was information about
microwaving PEG solutions to artificially age new samples so that they would
crystallize like the older PEG's. So I would infer that heat does have a
significant effect on solid PEG's. All PEG's with MW >=600 are solids at r
Dear all,
I'm finishing a refinement using SHELX and Coot (1.3A) and I have a modified
Arginine. There’s a blob of positive density (9.04 and 7.01 sigma) binding NH2
in the 2 conformations. I think it could be a hydroxyl there.
1) How can I add that in Coot?
2) Does SHELXL recognise modified
1) Do you have a line:
Option "Stereo" "10"
in the "Screen" section of your xorg.conf?
2) Is the 3D Vision emitter hooked up both to a USB port _AND_ to the
mini-DIN stereo socket on the Quadro card? AFAIK emitter sync with only
USB connection is not supported under Linux.
http://htt
Tim,
I'm shooting from the hip here, but I think the problem is that cctbx
comes with its own python, which you would need to run both pymol and
numpy under. According to Ralf it is at least not trivial to utilize the
system python to run cctbx. So I think you need to compile/install pymol
against
Dear all,
I've been trying to install the SuperSym module for pymol (svn trunk version of
pymol as of today, 1.3.x). Upon restart the console says "Ooops! SuperSym
requires cctbx and numeric python to function. Please install these."
The system is i7 with Debian Testing 64bit with python2.5 (alt
I recently ran into a similar case where the SG was P2(1)2(1)2(1) with a
~ b (within a few angstroms), thus emulating a P422 metric symmetry.
Full details here: Pubmed ID: 20057079
As Ian says, sometimes the spot splitting was particularly visible,
sometimes it was not. SAINT was not able to i
The meting point of PEG 1000 is around 38C. Obviously, if Sigma has
heated the batch to fill the bottles in the first place this is a futile
exercise... I'd ask them first.
Flip
Vellieux Frederic wrote:
R.Srinivasan wrote:
Dear All,
I have got initial crystals in a condition with
My experience with pseudo-merohedral twinning (it was actually the
reticular case with half the spots overlapped and the other
non-overlapped half on a pseudo C-centred lattice) is that the degree
of splitting varies widely over the diffraction pattern. In some
places there was complete overlap,
On Tue, Jun 22, 2010 at 11:09 PM, wrote:
> My interest was really what happened in the observed diffraction
> pattern. With the large difference in the orthorhombic cell dimensions,
> the spots will gradually separate for the higher orders. The point I
> really wanted to discuss was whether ther
On Wed, Jun 23, 2010 at 12:40:35PM +0530, R.Srinivasan wrote:
> Dear All,
>
> I have got initial crystals in a condition with PEG 1000. The PEG
> 1000 stock we had in our lab was rock solid and when i heated it to
> about 50 degrees for 15 to 20 minutes it became a solut
R.Srinivasan wrote:
Dear All,
I have got initial crystals in a condition with PEG 1000. The
PEG 1000 stock we had in our lab was rock solid and when i heated it
to about 50 degrees for 15 to 20 minutes it became a solution. We
thought the compound has got out dated or something like
Dear Tassos,
thanks for alerting us to this unexpected but welcome fact!
I would like to take the opportunity to
a) congratulate George Sheldrick!
b) point out to the CCP4 community that we decide ourselves about the
impact factors of journals that are important for our work:
specifically, if we
Dear All,
I have got initial crystals in a condition with PEG 1000. The PEG 1000
stock we had in our lab was rock solid and when i heated it to about 50 degrees
for 15 to 20 minutes it became a solution. We thought the compound has got out
dated or something like that and bought a bran
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