Sounds rather extreme considering what's /actually/ annoying you is you
weren't told up-front that's it's not worth your time trying to install
whatever you were installing. You should be complaining to whomever
misled you into wasting your week.
The other thing you seem to be railing against
Dear Natalie,
I try to run my images with fast_dp, but got the error message:
Fast_DP installed in: /home/lu/bin/fast_dp_20141205
Starting image: /home/lu/Documents/hg6l3/Hg6_L3_1_2.mccd
Number of jobs: 1
Number of cores: 0
Processing images: 1 -> 360
Phi range: 112.50 -> 472.50
Template: Hg6
Just an update. If I run shelxd from the command line the same error
appears. However, if I change the shelxd to the mp version, the command
line works but the hkl2map still doesn't work. I am more confused now.
Your input is greatly appreciated!
Best,
Chen
On Tue, May 12, 2015 at 5:11 PM, Chen
Dear Smith,
Here are some resources, I would then google around any topics or terms that
are unclear.
http://mcl1.ncifcrf.gov/dauter_pubs/284.pdf
http://www.ruppweb.org/Xray/comp/space_instr.htm
See page 3 for an example using P 1 21 1:
http://xray.tamu.edu/pdf/notes/guidetospacegroups.pdf
Ta
As other people have advised in response to some of your previous posts: Invest
in a copy of Bernard Rupp's fantastic text book. Judging from the number of
posts you make, you seem interested in learning the art of crystallography.
This book will answer most if not all of your questions
http://
Dear All,
Alhough there are on-line explainations on the space group, I found it was
difficult to fully understand. Here we take P 1 21 1 as an exmaple, will you
please explain to me with easy language what each number indicates？Or do we
have a on-line server which can demonstrate the meaning
Hi Clemens,
your suggested description of positive rotation doesn't remove the
ambiguity.
My intuitive way to define positive rotation (in 1994 or so, when
building the SBC) was:
Looking onto the sample, rotation of the sample in mathematically
positive direction
Only later I was told th
No, it is not sulfenic acid or so, I had that in differend structure. It is
L shaped from S, and linear if I put SCX mutaion (another 1.4A way a nice
blob). My resolution is 1.3 A.
On Tue, May 12, 2015 at 4:18 PM, Artem Evdokimov
wrote:
> Looks like a wrong shape for tetrahedral acid
> ...
> O
Hi Kay,
On Tue, May 12, 2015 at 08:39:24PM +0100, Kay Diederichs wrote:
> According to
> http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#ROTATION_AXIS=
> the definition of a positive value in the ROTATION_AXIS= line is:
>
> "When looking along the axis, the crystal w
On May 12, 2015, at 3:08 PM, Douglas Theobald wrote:
> On May 12, 2015, at 4:50 PM, wrote:
>> I like the open source model, but there are problems with this model along
>> with the others. One major problem is that the authors are expected to
>> support their software after others have gone in
Looks like a wrong shape for tetrahedral acid
...
On May 12, 2015 4:07 PM, "Boaz Shaanan" wrote:
> Hi,
>
>
> As I've just written to David, maybe it's sulfenic acid (result of
> radiation damage?). I've had those in some cases. See attached scheme for
> the chemistry and other possibilities for
Hi all,
I encountered a problem with shelxd (in hkl2map gui) installed in a flash
drive running 32 bit Ubuntu OS.
The error message is:
OMP: Error #29: Unable to set OMP thread stack size to 268435456
OMP:System error #12: Cannot allocate memory
OMP:Hint: Try decreasing OMP_STACKSIZE
The $OMP_ST
Making the software OSS solves many problems. For example, it solves the
problem of interdependency. Many tools these days aggregate the functions of
several different software packages into pipelines. If one step in that
pipeline is unavailable then the pipeline can be rendered unusable.
Most
On May 12, 2015, at 4:50 PM, wrote:
>
> "In practice, for me to be able to replicate and verify your computational
> analysis and results, I will need to be able to see your source code, compile
> it myself, and potentially modify it."
>
> Why? In this case to verify something you need to hav
On Tuesday, 12 May, 2015 16:06:51 Douglas Theobald wrote:
> On May 12, 2015, at 3:19 PM, Robbie Joosten
> wrote:
> >
> > I strongly disagree with rejecting paper for any other reasons than
> > scientific ones.
>
> I agree, but … one of the foundations of science is independent replicability
>
Hi,
As I've just written to David, maybe it's sulfenic acid (result of radiation damage?). I've had those in some cases. See attached scheme for the chemistry and other possibilities for Cys modification by oxidation.
Boaz
Boaz Shaanan, Ph.D.
Of note, this discussion was recently in the pages of Nature:
http://www.nature.com/news/rule-rewrite-aims-to-clean-up-scientific-software-1.17323
Shane Caldwell
McGill University
On Tue, May 12, 2015 at 12:48 PM, James Stroud wrote:
> I hereby call on the broadest community of academics and r
"In practice, for me to be able to replicate and verify your computational
analysis and results, I will need to be able to see your source code, compile
it myself, and potentially modify it."
Why? In this case to verify something you need to have the same output for a
given input, this does not
On May 12, 2015, at 3:19 PM, Robbie Joosten wrote:
>
> I strongly disagree with rejecting paper for any other reasons than
> scientific ones.
I agree, but … one of the foundations of science is independent replicability
and verifiability. In practice, for me to be able to replicate and verify
So far almost everyone is suggesting BME.
I didn't do the purification & crystallization myself, but I am told:
Buffer was HEPES
cryo was ethylene glycol, glycerol and DMSO.
Some MgSO4 and KPO4
No BME, but maybe some DTT.
Purified from a proteobacterium.
On 05/12/15 15:20, Dyda wrote:
What
Dear all,
We invite you to our upcoming serial crystallography data analysis workshop
at ACA 2015 in Philadelphia, PA, entitled "Serial Crystallography Data
Analysis with Cheetah and CrystFEL: Concepts and Tutorials". The workshop
details can be found on the BioXFEL website (
https://www.bioxfel.o
According to
http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#ROTATION_AXIS=
the definition of a positive value in the ROTATION_AXIS= line is:
"When looking along the axis, the crystal would rotate clockwise when
proceeding to the next data image."
There is of cour
BME around ?
Jürgen
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab: +1-410-614-4
Smells like BME to me...
On May 12, 2015 2:32 PM, "David Schuller" wrote:
> What are the most likely modifications of a CYS residue? I am attaching
> images of a couple of residues in my current structure. Blue is 2Fo-Fc,
> Green is Fo-Fc positive difference, purple is model-phased anomalous
> di
I strongly disagree with rejecting paper for any other reasons than
scientific ones. A paper describing software should properly describe the
algorithms to ensure the reproducibility. The source should be available for
inspection to ensure the program does what was claimed, for all I care this
can
If the software were open source, then funding would not matter. It could be
supported (or at least used) by the user base. Withdrawing the use of published
software because of funding issues represents a problem that can be remedied by
enforcing (at the referee level) open source licenses.
We
Did they stop supporting it due to lack of renewed funding and having to
cut staff that had the knowledge?
I'm pretty sure you only know part of the story.
On Tue, May 12, 2015 at 11:48 AM, James Stroud wrote:
> I hereby call on the broadest community of academics and researchers,
> including s
On May 12, 2015, at 12:29 PM, Roger Rowlett wrote:
> Was the research publicly funded? If you receive funds from NSF, for example,
> you are expected to share and "make widely available and usable" software and
> inventions created under a grant (section VI.D.4. of the Award and
> administrati
Was the research publicly funded? If you receive funds from NSF, for
example, you are expected to share and "make widely available and
usable" software and inventions created under a grant (section VI.D.4.
of the Award and administration guide). I don't know how enforceable
that clause is, howe
OK. I guess I was thinking of subtracting 2fo-Fc maps, which would give
essentially (Fo1-Fo2) coefficients. But coming out of phenix it will be at
least 2mFo-DFc, with different m's and D's for the two datasets. Makes it
rather more complicated.
eab
On 05/12/2015 11:58 AM, Philip Kiser wrote:
Can you get a license ?
I know of several software that have components from other developers from
which one needs to obtain a separate license.
Was the discountinued software superseded by something more superior ?
Can you send me an off list reply including the software name ?
J?rgen
I hereby call on the broadest community of academics and researchers, including
scientists, historians, economists, sociologists, psychologists, and whoever
else has ever published a paper or read from the literature thereof, to reject
any and all papers that describe new software that itself is
Hi
As far as I am aware beamline BL17U at Shanghai has what we in the Mosflm world
call "reverse phi" (or in the XDS world you'd want to change the ROTATION AXIS
vector).
There are often good reasons (to the engineers who have installed the equipment
on the beamline) why the crystal rotation i
This seems like a good problem for SAXS rigid body modeling. We previously
used an approach based on docking models into SAXS envelopes with the
constraint of 2-fold symmetry, followed by scoring the dimer models using the
goodness of fit to the experimental curve (1). Another approach would
I not so familiar with data collection hardware! I still have a lot to learn.
This data set was collected from SSRF(Shanghai China). I don't know how they
rotate the spindle.
Can you provide me some reference material？
Best wishes!
--
卢作焜
南开大学新生物站A202
At 2015-05-12 22:41:24, "Kay Dieder
Yes! two data sets from one crystal with 2 different wave length.
--
卢作焜
南开大学新生物站A202
在 2015-05-12 22:14:16，"Huw Jenkins" 写道：
>Hi,
>
>Also the IXDREF.LP files from yesterday and today suggest that you are having
>problems with 2 different datasets. Is that correct?
>
>IDXREF from yesterda
You found it!
XDS.INP needs
ROTATION_AXIS=-1 0 0
with this setting, IDXREF indexes more than half of the reflections:
REFINED VALUES OF DIFFRACTION PARAMETERS DERIVED FROM 10956 INDEXED SPOTS
REFINED PARAMETERS: AXIS BEAM ORIENTATION CELL
STANDARD DEVIATION OF SPOTPOSITION (PIXELS)
Hi,
Also the IXDREF.LP files from yesterday and today suggest that you are having
problems with 2 different datasets. Is that correct?
IDXREF from yesterday had:
NAME_TEMPLATE_OF_DATA_FRAMES=/home/lu/Documents/StructurePro/images/luzk/Hg6/hg6_L1_1_?
OSCILLATION_RANGE=0.5000
X-RAY_WAVELE
On 12 May 2015, at 13:09, luzuok wrote:
> STANDARD DEVIATION OF SPINDLE POSITION (DEGREES) 11.13
Is the oscillation range and rotation axis direction correct in your XDS.INP
file?
Huw
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Natalie,
I usually look at the first frame with adxv and estimate the ORGX ORGY
(which can be different from the direct beam position) by eye based on
shadows (as Kay mentioned before) or ice rings and copy the values
into XDS.INP.
Regards,
Tim
Dear Natalie,
On Tue, May 12, 2015 at 02:08:42PM +0100, Natalie Tatum wrote:
> Dear Lu,
>
> Just last week I faced an almost identical problem: iMoslfm had no problem
> but XDS failed.
Yes - that happens often because the beam centre recorded in the image
header doesn't specify what coordinate s
Dear Lu,
Just last week I faced an almost identical problem: iMoslfm had no problem
but XDS failed. I discovered, as Kay has suggested, the ORGX and ORGY
values were incorrect in XDS.INP. In fact, they had essentially been
swapped. If you have AUTOINDEX.INP from fast_dp, you can compare the
values
Dear LU,
yes, your spot_15.png looks good. What worries me now is the table
INDEX_ QUALITY DELTAXD YD X Y Z DH
DK DL
ORIGIN
0 0 0 1.70.1997.7 1020.9 0.0010 0.0005 1.02190.38
0.510.25
0 -1 0 3.00.4
Dear Kay,
I've tune these parameter for many times, and I got best results . :
SPOT_RANGE=1 100
INCLUDE_RESOLUTION_RANGE=50 4.2
MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=20
but still got the same error message!
The SPOT.XDS file was ploted (see attachment "spot_15.png" ), it seems that t
Dear all,
I want to have a closer look at a conformational change in a multidomain
protein. We see clear changes from different structures but there is
evidence that the conformational changes might be larger than observed.
My idea is to get the transformation matrix of each residue (or of each
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