Hi Yuri,
To add something nobody else has mentioned yet.
If you are interested in statistics and analysis you may find
interesting the R package. There is an excelent module, called Bio3D for
the analysis of protein structure and sequence data. Have a look here:
http://bio3d.pbworks.com/w/page/78
Hi Yuri,
If you don't like Python, like myself (and I'm not alone, it
would seem), you could try Ruby (http://www.ruby-lang.org/en/). Some
examples of PDB file manipulation are below (taken from [1]).
The language is a great improvement in Perl and Python in my opinion, but
the downside
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 in
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 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
On Tue, Jan 24, 2012 at 10:24 AM, Ian Tickle 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 you are worki
On 24 January 2012 08:59, Tim Gruene 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 I've put off
learning P
On 12-01-24 09:36 AM, Ian Tickle wrote:
On 24 January 2012 14:19, David Schuller 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
I should know better than to touch a flame post, but, but here goes:
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 redundancies
alt
On 24 January 2012 14:19, David Schuller 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. Siebert, M. Stefik
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von
Delft
Sent: 24 January 2012 15:08
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] writing scripts-off topic
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
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 m
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 view
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 depe
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
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 201
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
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 ab
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 excelle
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 should I use python,C++, visual basic?
> thanks
Pyt
On 12-01-23 09:59 PM, Ethan Merritt wrote:
On Monday, 23 January 2012, 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,
Jens
-Original message-
From: Ethan Merritt
To: CCP4BB@JISCMAIL.AC.UK
Sent: 1970 Jan, Thu, 1 00:00:00 GMT+00:00
Subject: Re: [ccp4bb] writing scripts-off topic
On Monday, 23 January 2012, Yuri Pompeu wrote:
Hello Everyone,
I want to play around with some coding/programming. Jus
Hi Yuri,
for example, you can use cctbx for this. Using cctbx you can do somethings
as simple as b-factor statistics (see example below) or as complex as write
your own refinement program (phenix.refine can serve as an example).
Example: compute min/max/mean B-factor for all atoms and for CA atom
On Monday, 23 January 2012, 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?
What you descri
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
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