Original Message
Subject: Structure problem
Date: Tue, 13 Sep 2011 08:55:47 +
From: #HEW KAI LI KELLY#
Hi,
I am facing some problems in solving my structure now, so I am wondering
if anyone is able to give me any tips and tricks on this matter.
My protein-DNA complex st
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Dear Francis,
ad [1]: if you are going for neutron diffraction, you probably want the
ligand to have its hydrogens replaced with deuteria, rather than a
'heavy atom derivative' of your ligand. The scattering power for
neutrons does not correlate with
Dear ccp4,
I am refining one structure at low resolution (3.5 A). I solved the structure
in space group P622 by molecular replacement. The Rw/Rf after some cycle of
rigid body refinement in Refmac5 is 34/37. But when I am trying to refine with
Restrain refinement in Refmac the Rw is going down
Dear Members,
Is any one using NVidia NVision 3D Setup with active stereo in linux
distribution for crystallographic work? Which one would be the best choice
to set up, an active stereo or a passive stereo for crystallographic work?
Can anyone shade some details on this? I am planning to buy or bu
Hi,
did you use refinement strategy suitable for low (3.5A) resolution
(secondary structure restraints, Ramachandran plot restraints, proper ADP
parameterization, SA, etc etc...)?
If you send me the data and model files off-list I will have a look.
Pavel
On Wed, Sep 14, 2011 at 7:34 AM, Md
I run the Alienware OptX AW2310 on two of our 3D Linux workstations and it
looks spectacular. Make sure that you have a Quadro FX Nvidia video card
that is on the approved list (
http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html) with
3-pin stereo (3-pin stereo connector required f
Are you sure of the space group? P622 is much rarer than P6(x)22 where x > 0
Phil
On 14 Sep 2011, at 15:34, Md Shaik wrote:
> Dear ccp4,
>
> I am refining one structure at low resolution (3.5 A). I solved the structure
> in space group P622 by molecular replacement. The Rw/Rf after some cycle o
Hi,
On Wed, Sep 14, 2011 at 9:48 AM, Hena Dutta wrote:
> Dear Members,
>
> Is any one using NVidia NVision 3D Setup with active stereo in linux
Yes
> distribution for crystallographic work? Which one would be the best choice
> to set up, an active stereo or a passive stereo for crystallographic
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Dear Md. Munan Shaik,
a couple of aspects you might check:
- - first build the model AS MUCH AS POSSIBLE before running the first
refinement cycle
- - switch off automatic weight determination in refmac and use a low
weight (e.g. 0.005) and many cy
Hi all,
As you may recall, the Protein Data Bank in Europe (PDBe; pdbe.org) regularly
produces Quips, short stories about QUite Interesting Pdb Structures
(pdbe.org/quips). Quips address biologically interesting aspects of one or
more PDB entries, coupled with interactive graphics views and of
Dear All,
I am having problems when trying to run Pointless with input from
Denzo/Scalepack.
(1) Pointless refuses to work from the .sca file. The error message is:
CCP4 library signal mtz:File not identified as MTZ (Error)
CCP4MTZfile: open_read - File missing or corrupted: rn7e222test.sca
or
Hello All,
Is Table 6 of http://cci.lbl.gov/sginfo/hall_symbols.html the authoritative
mapping of space group numbers to Hermann-Mauguin symbols (i.e., can we count
on major software packages to honor this mapping if present in a PDB file)? I
notice that this web page was authored by a couple o
On Wed, 2011-09-14 at 14:06 -0400, Emmanuel Saridakis wrote:
> If
> not, is there another way to check my point group/spacegroup starting
> from
> Denzo/Scalepack?
>
If you are trying to choose the screw axes, you can always look at the
systematic absences. This script may be useful in extracting
Hi,
On Wed, Sep 14, 2011 at 10:52 AM, Hena Dutta wrote:
> Hi Sabuj,
>
> Can I use LED monitor instead LCD? I heard the color contrast is better. If
We haven't tried any, but here's an interesting 120 HZ LED monitor
(Acer HS244HQ):
http://www.newegg.com/Product/Product.aspx?Item=N82E16824009301&
On Wednesday, September 14, 2011 10:16:53 am James Stroud wrote:
> Hello All,
>
> Is Table 6 of http://cci.lbl.gov/sginfo/hall_symbols.html the authoritative
> mapping of space group numbers to Hermann-Mauguin symbols (i.e., can we count
> on major software packages to honor this mapping if pres
Dear colleagues,
Has anyone seen glycerol on a three-fold axis?
THis is possible as the glycerol can be disordered but I want to know if
there is an actual case.
Any information would be greatly appreciated.
Jackie Vitali
On 09/14/11 13:53, Sabuj Pattanayek wrote:
Hi,
On Wed, Sep 14, 2011 at 10:52 AM, Hena Dutta wrote:
Hi Sabuj,
Can I use LED monitor instead LCD? I heard the color contrast is better. If
What is being marketed as "LED" monitors recently are actually LCD
monitors which use LEDs rather than fl
On Wed, Sep 14, 2011 at 3:23 PM, Hena Dutta wrote:
> Hi,
>
> Isn't that an LCD monitor (Acer HS244HQ)?
It's edge LED backlit. I don't know if there are any direct LED
backlit 120Hz monitors. Couldn't find much information on those types.
I'm running into some geometry problems with my DNA model after refinement with
refmac (version 5.5.0109), and would appreciate any feedback.
The problem is that the angles for many of the glycosidic bonds are 2 to 4
degrees off of the ideal values, and so are several standard deviations outsid
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OK, I updated ccp4 to 6.2.0 (and refmac to 5.6.0117) and now the angles coming
out close to the ideal values. Also, I see now the the "MODRES" in the pdb
header from before was tell future refmac runs to rename those residues - which
confused the newer refmac version as it thought the DT (rename
Just echoing what has been said.
I would make sure you have the right space group.
It may be worthwhile tyring to find a MR solution in different space groups
with different compositions.
Another imporatant thing is how complete is your model?
Do you have all the protein and DNA modeled in? How ma
Dear colleagues,
I have a problem running procheck on Mac OS X 10.6.8. It stops with the
following error:
..
Stereochemical quality plots and residue-by-residue listing
At line 2639 of file
/sw64/src/fink.build/ccp4-6.2.0-101/c
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