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,
Yuri,
I second everythig Ethan Merritt said, but would add: awk is easier and as functional as Perl for
"quick and dirty" projects. Once you need Perl's complexity, you're probably better off
moving to Python or a compiled language; Perl is powerful, but it allows you to do really dirty
coding
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
Hi Sam,
some obvious questions:
1-Space group right? ( i´d say so from your R values...)
2-Is your data good throughout all of the 180 frames? whats Rsym if take only
100?
3-how good/complete is model? Missing parts, residues, base pairs??
4-evaluate your refinement strategy...
HTH
These R-values are reasonable:
http://xray.bmc.uu.se/gerard/supmat/rfree2000/plotter.html
On Mon, 2012-01-23 at 21:48 +, Sam Arnosti wrote:
> Hi every one
>
> I have some crystals in the space group P3121. I collect 180 frames of data.
>
> My crystals do not diffract better than at most 2
Hi every one
I have some crystals in the space group P3121. I collect 180 frames of data.
My crystals do not diffract better than at most 2.0 angstrom, but the Rf barely
goes below 23%,
and Rfree also remains somewhere between 28-33%. I have tried to refine my data
as much as I can.
I do not
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 "configure" runs I'm told
checking for Gt
I would suggest MolProbity along with KiNG (on Firefox!) would be most
appropriate (http://kinemage.biochem.duke.edu/).
HTH,
Nadir
Pr. Nadir T. Mrabet
Structural& Molecular Biochemistry
N-gere - INSERM U-954
Nancy University, School of Medicine
9, Avenue de la Foret de Haye, BP 184
54505 Vand
You can use Ncont or distang to get all contacts then farm the output
for ones you want.. By N O ansd C do you mean main chain atoms only or
all such links?
I am a great grep expert to do things such as this.
Eleanor
On 01/22/2012 06:47 PM, REX PALMER wrote:
Can anyone recommend a program th
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