Dear all,
is there a simple way for a local installation of a wiki (in particular the
pymol wiki)? Our working network is physically separated from the internet and
going back and forth between computers just to look up a single command is
rather time consuming.
Thanks a lot, Tim
P.S.: I am
(just forwarding this to the list...)
Dear Tim,
I think it may be possible, though rather long-winded to do. First of all,
you'll need a working installation of mediawiki. My suggestion to get this
would be to download one of the self-contained installations available from
bitnami:
Hi Pu
Obviously your SAD SIRAS solutions can't both be right, one must
have the inverted handedness: I would guess it's the SIRAS solution
that's wrong, since the SAD solution seems to have given you an
interpretable map. The reason for getting the wrong hand in the SIRAS
case is probably that
Maybe I need to elaborate on Ian's answer.
SHELXD or other heavy atom location programs based on Patterson and direct
methods have a 50% chance of getting either heavy atom enantiomorph,
and in addition different solutions may be related by allowed shifts of
the cell origin (8 in P212121).
Dear Pro. George,
Many thanks for your detailed and clear exposition, which gives me a more
clear idea about this question (Although I still don't really understand the
basc mathematic things behind it).
I rechecked the sharp logs, and found that the original SAD sites were
wrong, which
Hi all,
I am trying to use PHASER in space group P1. I has expected that PHASER would
have centered the first protein molecule or at least placed an atom at the
origin of the P1 unit cell. Is this how PHASER works or am I mistaken?
Thanks for your help.
Ray
ray-br...@att.net
MAD and SIRAS will in general behave like SAD. However if your isomorphous
difference is large and the anomalous signal is lost in the noise, they
might be dominated by it and so tend to behave more like SIR.
I thought that MAD and SIRAS had no hand ambiguity--not true?
Jacob Keller
Not true. For MAD and SIRAS you still have to try both hands of the heavy
atom substructure (unless the heavy atom arrangement is itself
centrosymmetric, then both hands are correct).
Maybe I should also mention for completeness, that for the space groups
I41, I4122 and F4122 the heavy atoms
Dear Pu,
sorry for the long(ish) answer ... handedness/enantiomorph, heavy atom
sites and consistency (while using SHARP/autoSHARP) are just one of my
favourites ;-)
On Fri, Aug 20, 2010 at 01:39:58PM +0100, Pu Gao wrote:
I rechecked the sharp logs, and found that the original SAD sites
were
Dear Colleagues,
Has anyone experienced difficulty in installing CCP4MG (2.4.1) with Windows7?
The symptoms when I try to use it, after an apparently ok installation, are:-
The tool bar remains as feint text but still allows a drop down menu.
Then trying to open a coordinate file (either from a
Dear all,
My case seems to have two factors: 1. origin choice. and 2.
handedness/enantiomorph.
And this kind of problem seems to be very common during the experimental
phasing process. And I learned a lot informations both theoretical and
practical from your replies.
Many thanks for all
That must be a bug..
2.00 is the lowest value permitted .
Possble causes: You have very low resolution data, and the overall B
value is badly estimated (not very common)
common cause: you have done TLS refinement which reports b value
differences from the TLS derived values. If you start
Dear Pu,
If I may add a few remarks those already made by George and Clemens, I
would say that you cannot expect two heavy atom solutions obtained in
separate runs of SHELXD (or any other substructure solution program) from
two distinct sets of differences to be consistent with each other in
Tim,
In general, the best way to go is to contact the owner and ask for an
SQL dump. It'll save far more time and frustration than scraping the
wiki. You can then use mysqlimport to import the dump into your
system. After that, copy the media files over and you should be set.
Make sure you
Dear Eleanor at al,
On Fri, Aug 20, 2010 at 05:20:05PM +0100, Eleanor Dodson wrote:
There is quite a lot of background to these Qs in a variwty of text
books, and something on this website.
http://www.ccp4.ac.uk/dist/html/pxmaths/index.html
Nice page :-)
When changing hand you need to
Is there a program that will read in a pdb coordinate file and re-order the
side chain atoms in each residue according to a standard order?
I've a program that compares two files for the same structure, but requires
that the order of the atoms be the same in both cases. I'm using a variety of
On Friday 20 August 2010 08:53:23 am Eleanor Dodson wrote:
That must be a bug..
2.00 is the lowest value permitted .
Possble causes: You have very low resolution data, and the overall B
value is badly estimated (not very common)
common cause: you have done TLS refinement which reports
The present generation of high throughput structural biologists stays on the
intellectual shoulders
of the giants of crystallography from past days (modifying GOOGLE). In the
military jargon, in the constant wars with the
structures, situation described in this exchanges is called encounter.
Ed Pozharski wrote:
On Fri, 2010-08-20 at 18:50 +0200, Charles W. Carter, Jr wrote:
Is there a program that will read in a pdb coordinate file and re-order the
side chain atoms in each residue according to a standard order?
I've a program that compares two files for the same structure, but
Hi Charlie,
Are you sure refmac won't sort this out for you ? If you just read the odd file
in and write it out doing zero cycles, won't the atoms be ordered in the pdb
convention ? Or is it O that does the trick or CNS?
Cheers,
Boaz
- Original Message -
From:
The Alber lab at UC Berkeley is pleased to release of the code for
Ringer version 1.0 (http://ucxray.berkeley.edu/ringer.htm). Ringer is a
program to detect molecular motions by systematic X-ray electron-density
sampling. The aim of Ringer is to go beyond static structural snapshots
of
Hi -
Got a new computer, was trying to install CCP4 following the Scott Lab
page (64 bit install) -
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/64-bit_Fink_for_10.5_and_10.6
First had to install fink - tried to follow that page, but didn't have the
cvs command (forgot about the xcode,
Hi David:
I think you need to start with the pure 64-bit fink from cvs in order to
get this to work. All the errors are a consequence of using the 32-bit
version. You can't mix them. I have no idea why they still don't have a
binary installer, but they don't.
Email me directly if you need
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