We're trying to solve a 50% twin crystal by experimental phasing (SAD & SIRAS)
since molecular replacement hasn't worked. The crystals diffract very well in
apparent space group P62 2 2. A Hg derivative shows a strong apparent anomalous
signal (from half-dataset correlations etc), but we've fail
Dear all,
a student doing a practical training course at the MX-group at BESSY II in
Berlin is looking for an internship in London:
Hello,
I study Biochemistry (diploma) at Freie Universität Berlin and I am in my
eighth semester.
At the moment I intern at MX-group at BESSY II Helmholtz Zentrum Be
Hi Amit,
you can manually define the range of a spectrum in PyMol:
spectrum [parameter], [spectrum type], minimum=[min], maximum=[max]
--> if you want to color according to B-factor this will translate to
e.g. :
spectrum b, blue_white_red, minimum=0, maximum=50
hth, Arjen
On May 12, 2011,
Hi Amit,
you can manually define the range of a spectrum in PyMol:
spectrum [parameter], [spectrum type], minimum=[min], maximum=[max]
--> if you want to color according to B-factor this will translate to
e.g. :
spectrum b, blue_white_red, minimum=0, maximum=50
hth, Arjen
On May 12, 2011,
I'm trying to install ARP WARP on my mac and I'm getting the following error
message. I installed the latest ccp4 and ccp4i from disk image.
Thanks for your help,
Kendall Nettles
Checking CCP4 & ARP/wARP installation -
One of the variables $CBIN, $CCP4_SCR or $BINSORT_SCR is not define
On 05/12/2011 08:13 PM, Fulvio Saccoccia wrote:
Dear ccp4 users,
I need to generate intensities from a model (.pdb). That is, I think that a
correct procedure could be to convert model to structure factor and then obtain
intensities squaring the SF.
Does anyone know how can I do?
Thanks in advan
Hello Kendall,
On May 13, 2011, at 2:14 PM, Kendall Nettles wrote:
> Checking CCP4 & ARP/wARP installation -
>
> One of the variables $CBIN, $CCP4_SCR or $BINSORT_SCR is not defined
> Please check your CCP4 installation
>
> Please check your ARP/wARP and CCP4 installation
This error appears
That would tale you half the way there. You then have to apply a reverse Lp
correction to get a number within a scale factor (diffraction volume, angular
velocity) of an ob servable quantity - assuming that's the goal.
Sent via BlackBerry by AT&T
-Original Message-
From: Eleanor Dodso
First off, thanks to all those who sent me their suggestions, a great
variety indeed. Here's the summary:
- turbo-frodo can do local rotamer optimization based on environment.
- SCRWL and WHAT-IF are servers for homology modeling
- Swiss PDB viewer/DeepView can also do homology modeling, but no
Dear all,
I am working on a high glycosylated protein, which was produced from HEK293
cells. Last time I added glycosylation inhibitor, the protein could exist some
monomers and dimers in a buffer pH5.4. This time I didn't add glycosylation
inhibitor, the protein seems highly aggregated and
Dear all,
I get this unexpected (by me) message from MrBUMP:
Reindex Warning: spacegroup P43212 does not have an enantiomorph
I thought P41212 and P43212 were enantiomorphs...
So, am I wrong ?
(PS: I'm looking for indications on how to use MrBUMP on a cluster with
a SGE queueing system. Any poi
Hi Wei,
Glycosylation usually stabilize proteins although it is a source of
structural heterogeneity for us crystallographers.Since you are expressing
in HEK293 cells, there is a strain of cells that is deficient for
glycosylation (it was designed by Gobind Khorana at the MIT I believe). You
may w
Does anyone know how to select an atom and rotate the image about this point in
Rasmol?
Rex Palmer
Birkeck College
On May 12, 2011, at 4:00 PM, CCP4BB automatic digest system wrote:
Hey all,
I would like to introduce point mutations in a structure and quickly
(and dirtily) minimize the new residue. (Best rotamer dependent on
local environment, or the like.) What are simple approaches that
don't
involve
Dear all,
I would appreciate it if anyone could provide me with a copy of this research
paper (PDF file):
J. Appl. Cryst. (2009). 42, 743-744[ doi:10.1107/S0021889809021700
(http://dx.doi.org/10.1107/S0021889809021700) ]
Rigorous filtration for protein crystallizationThank you so much !
Rex,
Issue the command 'center [_expression_]'
For example 'center asp44:a.ca' would center rotation about
c-alpha of Asp44 in chain A.
Cheers.
On 5/13/2011 3:56 PM, REX PALMER wrote:
On a similar extension to this topic, is there a good software out there for
doing these kinds of modifications and minimizations for protein structures
with chemicals entities (i.e., protein/inhibitor complexes). What I am looking
to do is take a protein/inhbitor complex and add chemical modifi
I wouldn't consider your case as the extension of the previous problem. Here
your goal is to change the ligands/chemical entities and not the protein.
For your problem, I would prefer to go in following steps,
Step 1: Make different modifications of small molecules according to your
choice unle
I thought so too It seems to me that there is a typo in the spacegroup
name in the code. I'll send you some fixed files offline.
Ronan is the expert on queueing systems, but I though the keyword "CLUSTER"
should be enough. It is supposed to work with SGE. There also seems to be an
undocume
On May 13, 2011, at 4:00 PM, Tom J. Brett wrote:
On a similar extension to this topic, is there a good software out
there for doing these kinds of modifications and minimizations for
protein structures with chemicals entities (i.e., protein/inhibitor
complexes). What I am looking to do is t
20 matches
Mail list logo
