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
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
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
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
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 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
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
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
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
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
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,
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
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