OK, feel like I need to comment on this one. In terms of general
programming you could use whatever you like, perl (if as was said
above you like write-only programs) tcl, python, c++ etc.
However if you would like to do crystallographic calculations, I can
recommend that Python + CCTBX is
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Dear Yuri,
if there is somebody near your office who knows the language XYZ pretty
well, go ahead and use that language. It's probably worth a lot more
having somebody to discuss your code with than to try and find a
consensus from people's opinion
If you know C++, I've found Kevin Cowtan's Clipper libraries very useful for
doing little analyses involving coordinate superposition, etc. I'm not sure I
would recommend learning C++ just for this purpose (though it's a good language
to know). Clipper is distributed in CCP4
Phil
On 24 Jan
Those people considering running faster code should consider using GPGPUs.
Advantages of GPUs are that they have many more cores than CPU. The
disadvantages are that the communication between the CPU and GPU is slow and
memory management is tricker. Thus there is no guarantee that code will
Hi,
Le lundi 23 janvier 2012 23:29:39 vous avez écrit :
On Jan 23, 2012, at 9:46 PM, Yuri Pompeu wrote:
Hello Everyone,
I want to play around with some coding/programming. Just simple
calculations from an input PDB file, B factors averages, occupancies,
molecular weight, so forth... What
On 23/01/12 19:49, Dale Tronrud wrote:
Hi,
I'm having trouble building Coot on a Gentoo system. When I try to
perform a SSM overlay I am told that I need to build the program with
libmmdbssm. I can't find a Gentoo package that provides libmmdbssm but
there is a libmmdb and a libssm. When
On 24/01/12 04:46, Yuri Pompeu wrote:
Hello Everyone,
I want to play around with some coding/programming. Just simple calculations
from an input PDB file, B factors averages, occupancies, molecular weight, so
forth...
What should I use python,C++, visual basic?
thanks
Yuri,
My 2c...
It
The European Molecular Biology Laboratory (EMBL) and the European
X-ray Free Electron Laser (XFEL) at DESY, Hamburg, Germany, have a
keen interest in the development of FEL-based applications in
structural biology. Within this framework the EMBL, together with
international collaborators
Dear all
We may use a Honeybee 963 robot to screen crystallization conditions for
trypsin-containing protein samples and we are worried about robot
contamination by residual protease.
How do you normally clean robots when using this kind of sample? Your
suggestions/recommendations will be
On 01/24/12 00:41, Bart Hazes wrote:
I have used a number of languages and have found only one I really
disliked, that being perl. It is hard for me to imagine that this
language was developed by a linguist yet in my eyes it is the least
natural language from human comprehension point of
Trigonal space groups have a choice of two arbitrary settings.
Were all those 180 frames collected in one pass? What were the
integration statistics?
What was the phasing method? Did you have a pre-existing structure*,
molecular replacement, anomalous, or what?
* This is the one I am
What an astonishingly low bar
On 24/01/2012 14:19, David Schuller wrote:
On 01/24/12 00:41, Bart Hazes wrote:
I have used a number of languages and have found only one I really
disliked, that being perl. It is hard for me to imagine that this
language was developed by a linguist yet in
It would seem that you have a large model bias. Rule of thumb is to keep
R/Rfree within 5% of each other. If you find that the numbers are separating
during refinement you need to reduce the weighting factor (dont use automatic)
during refinement. What is your overall redundancy? Higher
On Tue, Jan 24, 2012 at 1:38 AM, Adam Ralph adam.ra...@nuim.ie wrote:
CUDA is a set of extensions for C which will allow you to access hardware
accelerators (certain NVidia cards in this case). CUDA has been around for
a
while and there are CUDA libraries for FFT and BLAS.
I have not
We have a Honeybee system but do not usually use proteases. The biggest
problem we have found is that if anything precipitates in the tips they have to
be washed very well, usually with water or ethanol. The ceramic tip can be
washed using low concentrations of HCl (0.1M), which I believe
Hi Horacio,
we have a Cartesian Honeybee and perform trypsin-containing trials by setting
up drops with a dedicated protein+trypsin tip, which we then wash extensively
with water, 6 M guanidinium hydrochloride, then water, isopropanol and again
water.
hth,
ciao,
Sebastiano
On Jan 24, 2012, at
Another vote for python+cctbx.
And a bit of fun:
http://xkcd.com/224/
http://xkcd.com/297/
http://xkcd.com/353/
http://comicjk.com/comic.php/217
http://comicjk.com/comic.php/823
http://comicjk.com/comic.php/842
http://comicjk.com/comic.php/849
From: CCP4 bulletin board
I realize the list is large and I don't want to clutter inboxes, but
anyone who may be lightly considering GPU implementations should
understand that this technology, while useful for some applications, is
probably not economical for crystallography refinements. I do not have
personal programming
Dear everyone,
I am trying to clone a viral protein in the E. Coli BSJ strain and i am
having some problems.
I start from the viral RNA carrying out a reverse transcription and PCR
(RT-PCR) to obtain the protein cDNA. When I sequence this cDNA to check for
mutations, there are no mutations. So
On 24 January 2012 14:19, David Schuller dj...@cornell.edu wrote:
On 01/24/12 00:41, Bart Hazes wrote:
www.cs.siue.edu/~astefik/papers/StefikPlateau2011.pdf
An Empirical Comparison of the Accuracy Rates of Novices using the Quorum,
Perl, and Randomo Programming Languages
A. Stefik, S.
I think the explanation is this:
The source is natural viral RNA which is a mixture of naturally mutated
sequences (e.g. flu forms such a quasispecies)
See:
http://www.virology.ws/2009/05/11/the-quasispecies-concept/
The pooled RNA has an average sequence that you see when you sequence the
pooled
On 24 January 2012 15:23, Greg Costakes gcost...@purdue.edu wrote:
It would seem that you have a large model bias. Rule of thumb is to keep
R/Rfree within 5% of each other. If you find that the numbers
are separating during refinement you need to reduce the weighting factor
(dont use
On 12-01-24 08:39 AM, Regina Kettering wrote:
We have a Honeybee system but do not usually use
proteases. The biggest problem we have found is that if
anything precipitates in the tips they have to be washed
very well, usually
I should know better than to touch a flame post, but, but here goes:
flame
don't use anything but python. They are nightmare languages, sloppy, and force
you to format the code by inserting semantically redundant brackets and
semicolons in a specific way rather than dispensing these
Is this observation about redundancies a general rule that I missed?
It seems rather surprising to me. What have results have others seen?
Dale Tronrud
On 01/24/12 07:23, Greg Costakes wrote:
snip...
Higher redundancies (7 or so) do tend to increase overall R/Rfree.
snip...
On 12-01-24 09:36 AM, Ian Tickle wrote:
On 24 January 2012 14:19, David Schullerdj...@cornell.edu wrote:
On 01/24/12 00:41, Bart Hazes wrote:
www.cs.siue.edu/~astefik/papers/StefikPlateau2011.pdf
An Empirical Comparison of the Accuracy Rates of Novices using the Quorum,
Perl, and Randomo
Whoops, I misspoke... I meant Rsym and Rmerge increase with higher
redundancies.
---
Greg Costakes
PhD Candidate
Department of Structural Biology
Purdue University
Hockmeyer Hall, Room 320
240 S. Martin Jischke
Inspired by the recent post about quasispecies:
I have been bothered recently by the following problem: why do species
of genetic uniformity exist at all (or do they?)? This first came up
when I saw a Nature paper describing live bacteria extracted from a
supposedly 250-million-year-old salt
On 24 January 2012 08:59, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
[flame=;-)]
P.S.: don't use python. It's a nightmare language, sloppy, it forces you
to format the code in a specific way rather than your own way and ...
[/flame]
I'm inclined to go along with you there: the main reason
Whoops--I meant to change the subject line, so if you want to reply,
please use this one not to perturb the original post.
JPK
Inspired by the recent post about quasispecies:
I have been bothered recently by the following problem: why do species
of genetic uniformity exist at all (or do
On Tue, Jan 24, 2012 at 10:24 AM, Ian Tickle ianj...@gmail.com wrote:
reassuring air of finality! Maybe a Python expert will answer this
but I've often wondered, what happens if as some editors do
(particularly if as I do you have to use different editors at
different times depending on where
On Jan 24, 2012, at 11:24 AM, Ian Tickle wrote:
Maybe a Python expert will answer this
but I've often wondered, what happens if as some editors do
(particularly if as I do you have to use different editors at
different times depending on where you are working, such as on Windows
working
Thanks everyone for your responses. I've tried to summarize the suggestions
and feedback from this thread:
- This was a very small sample size, but overall ConturELN
(http://www.contur.com) from Accelerys was the most popular option, followed by
Labguru (http://www.labguru.com). Two others
El 24/01/12 18:56, Greg Costakes escribió:
Whoops, I misspoke... I meant Rsym and Rmerge increase with higher
redundancies.
But then suppose that one merges data from a crystal that is degrading
while exposed, sp the data gets degraded. This is not at all unusual. In
the absence of a deep
When did writing scripts become off topic for the CCP4BB!?
Personally, I use awk for most text-processing tasks, and since I have
found that ~95% of science is converting information from one file
format into another, I tend to use awk a lot.
The k in awk stands for Kernighan, one of the
On 01/24/12 11:52, Miguel Ortiz Lombardia wrote:
El 24/01/12 18:56, Greg Costakes escribió:
Whoops, I misspoke... I meant Rsym and Rmerge increase with higher
redundancies.
But then suppose that one merges data from a crystal that is degrading
while exposed, sp the data gets degraded.
I am looking for a program/server that would determine secondary
structure from a pdb file and then output a new pdb file with
HELIX/SHEET records. I have a model for which pymol fails to produce
correct secondary structure. DSSP and STRIDE identify the secondary
structure correctly but I'd need
Try DSSP2PDB.
http://structure.usc.edu/dssp2pdb/
It's a perl script.
Crossover flame note: I spent a lot of time learning perl and I still don't
recommend the language ;-)
James
On Jan 24, 2012, at 1:57 PM, Ed Pozharski wrote:
I am looking for a program/server that would determine
You can try STRIDE2PyMOL:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/stride_ss.py
/Martin
On Jan 24, 2012, at 9:57 PM, Ed Pozharski wrote:
I am looking for a program/server that would determine secondary
structure from a pdb file and then output a new pdb file with
HELIX/SHEET
On 12-01-24 11:20 AM, Jacob Keller wrote:
Inspired by the recent post about quasispecies:
I have been bothered recently by the following problem: why do species
of genetic uniformity exist at all (or do they?)? This first came up
when I saw a Nature paper describing live bacteria extracted from
This reminds me of stride2pdb in case you want to use more than pymol with your
secondary structure assignments:
http://structure.usc.edu/stride2pdb/
James
On Jan 24, 2012, at 2:20 PM, Martin Hällberg wrote:
You can try STRIDE2PyMOL:
Dear All,
I wrote a story about the catalysis of Acetoacetate Decarboxylase. It
is available here:
http://www.jinkai.org/AAD_history.html
http://www.jinkai.org/AAD_catalysis.html
I wish you will like it.
Regards,
Kevin
Oh, and don't fall for the so other people can read your code trick.
Trust me, NOBODY wants to read your code! Unless, of course, they are
trying to re-write it in their favorite language.
I don't think this is necessarily the case. If I'm using your code to
do something scientifically
Dear All,
I got this email. Is my account blocked?
Thanks,
Kevin
2012/1/24 asch...@cipf.es:
Esta cuenta de correo electrónico dejara de existir dentro de 6 meses
(25/05/2012).
Si desea ponerse en contacto con el titular de este correo hágalo a través
del siguiente e-mail:
On Jan 24, 2012, at 4:00 PM, Ed Pozharski wrote:
I am looking for a program/server that would determine secondary
structure from a pdb file and then output a new pdb file with
HELIX/SHEET records. I have a model for which pymol fails to produce
correct secondary structure. DSSP and STRIDE
Rubén,
the previous answer probably addresses your problem accurately.
However. If your protein of interest modifies DNA/RNA, it is quite common that
your pET constructs will mutate rapidly in E.coli. Lac operons tend to leak
quite a bit, which is not enough to detect the protein prior to
El 25/01/12 01:19, Kevin Jin escribió:
Dear All,
I got this email. Is my account blocked?
Thanks,
Kevin
2012/1/24 asch...@cipf.es:
Esta cuenta de correo electrónico dejara de existir dentro de 6 meses
(25/05/2012).
Si desea ponerse en contacto con el titular de este correo
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