I presume the Quadro 4000 should work, it is listed on the supported
products page:
http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html
We have a Quadro FX 3800 card with the optional stereo bracket
(900-50762--000).
http://www.bhphotovideo.com/c/product/652465-REG/PNY_Techn
Hi Florian,
There are quite a few tools that do this check for you. To name a few: WASP
(old but good, build the ion as water), WHAT_CHECK
(http://swift.cmbi.ru.nl/servers/html/index.html), Check My Metal and
probably quite a few others. All of them use the bond valence sum, but they
all have a di
Dear CCP4BBers,
I'm refining the structure of a Ca-binding protein with several EF-hands
against 2.2A data.
There is clear density for an ion in several EF-hands coordinated by
Asp/Glu, Ser, one backbone O and one water (coordination number 5 and
6). Ca2+ can be excluded as there are no anomal
Herbert foundd that one is allowed to vote once per day
so that would be a good way to boost his count. Note
that Bill is currently in second place and only a few
hundred votes behind so getting him to the top should
be doable.
Frances
===
Hi Fellows,
here is your chance to vote for a crystallographer in the People's Choice
education program contest:
http://us2.campaign-archive2.com/?u=3e43dd9d1724b97d2bc286881&id=485f01c36b&;
e=76452e4682
Best regards, BR
-
Bernhar
The center bit looks very much like phosphate - see what happens if one
is placed there
It may be educational to look at the maps in P1, just to see how much
trouble is caused by "noise accumulation on the symmetry axis"
On Thu, 2011-12-01 at 09:36 +, Martin Montgomery wrote:
> Posting on beh
On Thu, 2011-12-01 at 16:33 +0100, Michael Hothorn wrote:
> Dear all,
>
> sorry for the off topic question (that has been asked many times before,
> but the hardware keeps changing): I want to buy a linux workstation with
> Nvidia 3D vision and an Alienware OptX AW2310 23-inch 3D TFT monitor.
>
I would also suggest using MolProbity to assess structure quality.
Best,
Nadir
Pr. Nadir T. Mrabet
Structural& Molecular Biochemistry
Nutrigenex - INSERM U-954
Nancy University, School of Medicine
9, Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Nancy Cedex
France
Phone: +33 (0)3.83.
For drawing a 2D fold topology I'd suggest TopDraw (
http://www.ccp4.ac.uk/html/topdraw.html). To see if you structure looks
like other structures I'd look at the DALI server (
http://ekhidna.biocenter.helsinki.fi/dali_server/). Dali is pretty good for
digging out results/discussion fodder because
Dear all,
sorry for the off topic question (that has been asked many times before,
but the hardware keeps changing): I want to buy a linux workstation with
Nvidia 3D vision and an Alienware OptX AW2310 23-inch 3D TFT monitor.
This set-up suggested by the CCP4 wiki for TFT stereo. Has anyone a
This was resolved offline. It turns out that there's an obscure bug in Phaser
triggered if you search for the same model twice as an alternative for itself
(e.g. "SEARCH ENSEMBLE ensemble1 OR ENSEMBLE ensemble1 NUM 1"). When the input
was fixed ("SEARCH ENSEMBLE ensemble1 NUM 1"), Phaser didn'
Stuck email... try again...
Original Message
Subject:Re: [ccp4bb] sugar and coot
Date: Wed, 30 Nov 2011 19:42:54 +
From: Paul Emsley
To: d...@iwonka.med.virginia.edu
CC: CCP4BB@JISCMAIL.AC.UK
On 30/11/11 17:07, Heping Zheng wrote:
The issue I hav
Dear Rex,
if you display hydrogens in Pymol you should be able to draw distances between
any atoms
(select the 2 atoms of interest with Ctrl + middle mouse, and type "distance"
into the command line).
However, one should obviously keep in mind the geometry of the free electron
pairs to which H
I think a metal ion is unlikely given that the
nearest ligand(s) are Arg residues. I would lay money on an anion.
The central feature looks very much like a bicarbonate ion,
and is very similar to the bicarbonate ion bound in a generic anion
binding site near 2 Arg re
I am looking for a program that will display weak CH---N bonds.
The programs I know about only display classical hydrogen bonds such as OH---N
etc.
Any suggestions please?
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
Well - first thing to do is an DANO map and see if it is a metal ion.
The relative height of the DANO peaks for S and anything else can give
you some clues.
Eleanor
On 12/01/2011 10:20 AM, Carlos Kikuti wrote:
It's bang on the Y axis I'd just ignore it (treat it as just noise) and
work
We had a similar case in our Eib structure (2xzr), with large peaks on a
3-fold. We initially thought it was noise, but Andrei Lupas convinced us to
look more carefully, and it turned out to be chloride ion.
You could do an wavelength scan at a beamline looking for anomalous signal at
the lo
It's bang on the Y axis I'd just ignore it (treat it as just noise) and
work on the rest of the model. There seems to be some trouble in other parts of
it. (Had a similar case but at 3.5 A data). I wonder what is the gap between
Rfree and Rwork.
And I'm curious for what more experienced pe
although it is hard to see in 3 2D views, some of the tentacles appear
connected to the protein, could they result from some of the long Lys or Arg
side-chains not following the 4-fold symmetry? i.e. alternative conformations?
The density on the 4-fold may be ions, solvent, some metal ion? "Noise
Posting on behalf of Katia Baranova (see below). Any suggestions gratefully
received!
Hello,
we have a puzzling density and hope someone has an idea of what it may be.
The pictures of it are here:
http://www.mrc-mbu.cam.ac.uk/sites/default/files/images/mystery/top.png
http://www.mrc-mbu.ca
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