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Dear List,
since this probably comes up a lot in manipulation of pdb/reflection files
and so on, I was curious what people thought would be the best language for
the following: I have some huge (100s MB) tables of tab-delimited data on
which I would like to do some math (averaging, sigmas, simple
Try R. :)
http://www.r-project.org/
Eric
On Wed, Sep 12, 2012 at 10:32 AM, Jacob Keller <
j-kell...@fsm.northwestern.edu> wrote:
> Dear List,
>
> since this probably comes up a lot in manipulation of pdb/reflection files
> and so on, I was curious what people thought would be the best language
I always use FORTRAN for such tasks, especially if speed is important.
George
On 09/12/2012 04:32 PM, Jacob Keller wrote:
> Dear List,
>
> since this probably comes up a lot in manipulation of pdb/reflection
> files and so on, I was curious what people thought would be the best
> language for th
Le Mercredi 12 Septembre 2012 16:40 CEST, "George M. Sheldrick"
a écrit:
May I add a little personal joke to the serious remark by George.
This remembers me a discussion I had with Jorge Navaza, let's say 15 years ago,
about the programming language of the future.
(To a good approximation, 15
Ho,
A second the vote for OmpF, but many porins could do. Although it is a little
harder to purify from native membranes, OmpF has the advantage that it can be
crystallized in about 1-2 hours from a simple detergent solution with different
PEGs AND (!!!) it is as stable as a rock (you can drop
One thing to keep in mind is that there's usually a trade-off between
setup (writing and testing) and execution time. For one-off data
processing, I'd focus on implementation speed rather than execution
speed (in other words, FORTRAN might not be ideal unless you're already
fluent with it).
On Wed, Sep 12, 2012 at 7:32 AM, Jacob Keller
wrote:
> since this probably comes up a lot in manipulation of pdb/reflection files
> and so on, I was curious what people thought would be the best language for
> the following: I have some huge (100s MB) tables of tab-delimited data on
> which I woul
A similar remark was made to me by David Blow, while he was on sabbatical at
UNC in the 1980s, working with the UNC Computer Science Department and in a
moment of intense frustration with the overpowering ignorance of fortran and
the enthusiasm for Unix exhibited by that department.
Charlie
On
I agree with Pete. Moreover, Python doesn't have built-in statistic
functions but adding package (numpy and scipy in this case) is very simple.
Quentin
Le 12/09/2012 17:11, Pete Meyer a écrit :
One thing to keep in mind is that there's usually a trade-off between
setup (writing and testing) an
Hi Jacob,
As the preceding discussion has illustrated, there are obviously a
number of options, nearly all of which will work well for what you
describe. As Pete Meyer suggested above, the best language may be the
one you already know (I also echo his suggestion to test your code on
a small subset
On Wednesday, September 12, 2012 07:32:54 am Jacob Keller wrote:
> Dear List,
>
> since this probably comes up a lot in manipulation of pdb/reflection files
> and so on, I was curious what people thought would be the best language for
> the following: I have some huge (100s MB) tables of tab-delim
>
> For the specific purpose you list -
> input from tab-delimited data
> output to simple statisitical summaries and (I assume) plots
> - it sounds like gnuplot could do the job nicely.
>
I wasn't aware that gnuplot can do calculations--can it? I was probably
going to use it somewhere as a plotti
All you need is scipy library to get those pesky statistic functions :)
On 09/12/2012 11:11 AM, Pete Meyer wrote:
Python's relatively easy to learn, and more flexible than octave/R;
but it doesn't have the built-in statistic functions that octave and R
do.
> Why are you dis-ing python? Seems everybody loves it...
Depends on if you like the object model, some don't. In the end it
really boils down to what you're used to and what you've learned to
use.
Now is the time when I start waxing nostalgic about the "old days" when there
used to be entire threads on this bulletin board about Fortran format statement
syntax for parsing various files.and I read them with great interest
How did I get to be such a geezer?
-Original Message-
F
Hi everyone,
I am trying to show that a ligand underwent catalysis during a soaking
experiment.
One of the things I would like to show is the geometry of the ligand, bond
angles/lengths, dihedrals, etc...
One of my models has a hi-res of 1.18A and the ligand density is really clear
and complete.
Dear all,
Thanks for your cooperation.
Regards,
Sudipta.
Sudipta Bhattacharyya,
Senior Research Fellow,
Department of Biotechnology,
Indian Institute of Technology Kharagpur, India.
>
>
On Sep 12, 2012, at 9:11 AM, Pete Meyer wrote:
> That said, I'd take a look at python, octave or R. Python's relatively easy
> to learn, and more flexible than octave/R; but it doesn't have the built-in
> statistic functions that octave and R do.
import scipy
Now it does!
It is the lack of compatibility between different versions mentioned by
Ethan that really put me off learning PYTHON. In contrast, the
FORTRAN-66 program SHELX76 still compiles and runs correctly with any
modern FORTRAN compiler. The only significant 'new' features that I now
use are dynamic ar
Python sorting 1 records of 1 floats for each record, finding the max,
min, and mean of entire 100,000,000 32 bit float array (400 MB) on a 6 year old
white imac.
*11.6 seconds.
*This doesn't include the time to generate the 400 MB of random (normal) data.
Try it on your own comp
Hi,
Python, of course (if you know some basic math). Otherwise, Python and a
good math text book -:)
Pavel
On Wed, Sep 12, 2012 at 7:32 AM, Jacob Keller <
j-kell...@fsm.northwestern.edu> wrote:
> Dear List,
>
> since this probably comes up a lot in manipulation of pdb/reflection files
> and so
On Sep 12, 2012, at 1:00 PM, George Sheldrick wrote:
> It is the lack of compatibility between different versions mentioned by Ethan
> that really put me off learning PYTHON.
Python is backwards compatible. I have reams of code I wrote in python 2.3 that
still works in 2.7 without modificatio
Ethan,
I think majority of your complaints about python result from its very
purpose - to be readable/portable for the sake of facilitating rapid
implementation. There are many other languages that provide tools to
accomplish what Jacob wants to do (well, I would stay away from P''),
but pyt
On Wed, Sep 12, 2012 at 12:49 PM, James Stroud wrote:
> Also, python (aka python 2) and python 3000 (aka python 3) are considered
> two different languages. It's not reasonable to consider them one language
> and then complain that they are incompatible. Python 3 was created as a new
> language (a
You can do unrestrained refinement in refmac, at your resolution it may
be OK. If you want to keep protein restrained, you can either use
harmonic restraints or come up with a special cif-file for your ligand
with large esd targets. There is no direct way to tell refmac to
exclude specific r
Colleagues: Another country is heard from:
Since no one has mentioned MATLAB, let me mention it.
--Can easily do any math from 2+2 to matrix SVD etc.
--Statistics toolbox does most of what anyone would want.
--Lots of easy quick graphics that can be prettied up if needed.
--If you know FORTRAN, yo
Hi all,
I am currently trying to perform a quickscale in iMosflm 7.0.9 after I
integrate in an R 32 space group. Unfortunately, both Pointless and Aimless
are both giving me a best solution space group of P 43 3 2. After analyzing
the statistics, this cannot be correct. Other programs such a
I encourage trainees to learn a programming language that they
will help their careers beyond their short time in my lab. Many or
most of them will not continue in structural biology or even science.
For the moment, I am pushing python even though I am minimally
literate in it myself. They sho
On 09/12/2012 06:41 PM, Cosmo Z Buffalo wrote:
is it possible to force Aimless and Pointless to generate statistics
in a space group other than the one it predicts?
yes, but it's pointless to force Pointless
And if so, how would I do this?
I assume you mean doing it from imosflm. If so, go
On Wednesday, 12 September 2012, Cosmo Z Buffalo wrote:
> Hi all,
>
> I am currently trying to perform a quickscale in iMosflm 7.0.9 after I
> integrate in an R 32 space group. Unfortunately, both Pointless and Aimless
> are both giving me a best solution space group of P 43 3 2. After analyzi
I'd just use a decent shell scripting language (like zsh) in conjunction with a
unix tool like awk. But the gnuplot option sounds ideal.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
Universi
In case it helps… After you've done unrestrained refinement, you can use
prosmart to generate external self-restraints to the current conformation
(using the -self_restrain keyword). This is flexible - you can specify residue
ranges, and it works for protein, ligand, DNA/RNA, waters, etc. These
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