I would like to thank Justin for his summary of this topic, which I'm
sure many people found of interest, and is very much in the spirit of
the bulletin board.
I would just like to correct one factual error, in that it has been
possible to specify anisotropic resolution limits to MOSFLM
Choose another graph from the loggraph - it also gives the main chain
alone and the side chains alone (not so useful!)
Eleanor
Salameh, Mohd A., Ph.D. wrote:
Dear All,
I would like to prepare a plot showing the b-factor of only the alpha
carbon and/or the backbone atoms and I wonder if
I would like to have some comments on whether the maps before or after
truncation are better . (obviously the Rfactors will be lower for the
truncated data ..)
I suspect it iwill be completely anecdotal - but I confess to a gut
unhappiness about throwing out measurements..
eleanor
Pavel
The protein crystallisation facility at the Institute of Biotechnology
will organise a three-day practical course on protein crystallisation
techniques. The course is aimed at graduate students and post docs with
interest in structural characterisation of proteins. The course will
include
Hi Everyone,
I echo Andrew's thanks for the summary offered by Justin.
I would like to mention another way to trim anisotropic diffraction patterns of
the weak patches 'at source', as it were, in MOSFLM, by specifying a sigma cut
off applied to each image.
from the manual:
RESOLUTION [ lowres
Just to add my two ha'porth.
I discussed this some years ago with Garib, just after I'd added the
anisotropic cutoff to the resolution limits in Mosflm (mentioned by
Andrew below); as I remember (and this is an invitation to Garib to
contribute and correct me here!), the answer went along
Hi Ian,
snip
I think the fundamental problem is that some people are still very much
attached (pun not intended)
And none taken .-)
to their text-based e-mail client (Pine, Pico or whatever), and I
completely agree that on this BB we have to cater for the lowest common
denominator. If
Dear ccp4bb,
I have just installed ccp4 6.1.2 with ccp4i 1.4.2 on a MacBook Pro running OSX
10.5.8.
When I try to run Refmac5 (or phaser) I get the status starting in the GUI
but the program
fails to run and no log file is generated. I source:
/usr/local/ccp4-6.1.2/bin/ccp4.setup-sh
before
Dear All
- I am looking for a multiple alignment program that will work
with upper and lower case letters in the sequences and preserve them through to
the output. I used to use PILEUP but that is no longer supported here.
Any suggestions much appreciated.
regards
Charlie Bond's ALINE program
(http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/) can handle
upper/lower case sequences.
In the menu bar: Tools Alignment Align All Sequences does the job
(using clustalw as a back-end IIRC) without changing cases.
Best,
Stephen
2009/9/16 MARTYN SYMMONS
Many thanks to all of you who replied, many great suggestions and I'll
try to utilize some of your ideas very soon. Thanks, Mohd
Mohd A. Salameh, Ph.D.
Mayo Clinic Cancer Center
Griffin Cancer Research Building
4500 San Pablo Road
Hi Mohinder,
Are you having problems because the CCP4I_TCLTK
environment variable is not set correctly? From the shell, you can
check
~$ echo $CCP4I_TCLTK
/usr/local/bin
...so you should have a tclsh binary there:
/usr/local/bin/tclsh
Otherwise, check the troubleshooting
Dear all,
I have an atomic resolution (1.1#197;) structure of enzyme with the bound
cofactor NAD. During the analysis of the refined structure I found that
important double C=O bond of the cofactor in the active site was slightly
lengthened from standard 1.22#197; to 1.26#197;. Then I increased
On Wednesday 16 September 2009 11:19:11 Ivan Shabalin wrote:
Dear all,
I have an atomic resolution (1.1Å) structure of enzyme with the bound
cofactor NAD. During the analysis of the refined structure I found that
important double C=O bond of the cofactor in the active site was slightly
To judge the significance of the value of a bond length, you cannot rely
on global measures of precision. You need the standard uncertainty of this
particular distance in this particular crystal. Refmac will not perform this
calculation for you. Shelxl will. It is certainly more cumbersome
Hi Ivan-
Since you most likely have the data to back it up and I assume you have the
computational firepower to do it, why don't you run a full matrix refinement
in SHELX to get estimates of bond lengths and their deviations? It's worked
for me in calculating carboxylate C=O bond lengths to
Hi,
I am getting a problem to prepare a figure in PYMOL. I have 4 nearly
identical monomers in the AU sitting at the corners of a rectangle. The 2 front
monomers almost perfectly superimpose on the back 2 when I am looking along the
plane. I can see this view in O program. For some reason I
On Wed, 16 Sep 2009 16:57:18 -0700, Raja Dey deyra...@yahoo.co.in said:
Hi, I am getting a problem to prepare a figure in PYMOL. I have 4
nearly identical monomers in the AU sitting at the corners of a
rectangle. The 2 front monomers almost perfectly superimpose on
the back 2
Hi Raja,
On Wed, 16 Sep 2009 16:57:18 -0700, Raja Dey deyra...@yahoo.co.in wrote:
Hi,
I am getting a problem to prepare a figure in PYMOL. I have 4 nearly
identical monomers in the AU sitting at the corners of a rectangle. The 2
front monomers almost perfectly superimpose on the back 2
Dear Jose:
Please try putting this into /sw64/fink/dists/unstable/main/finkinfo/x11
it contains what is hopefully a fix to blt.
blt-x86_64.info
Description: Binary data
Thanks.
Bill
On Sep 15, 2009, at 4:43 PM, José Trincão wrote:
Hello all,
I upgraded my Macbook Pro to snow
Hi, All,
What's the general rules for selecting cryosolvent?I got crystals in 30%
PEG4000/PEG3350, 0.2M AS and 0.1M NaAC,how should I choose cryosolvent?
Thanks.
Rui
Hi Mohd:
The script below should also be able to edit the PDB file according to
both of your needs. Think it is also easily modified to use for other
similar PDB file editing needs.
Best wishes,
Navdeep
#
#! /usr/bin/gawk -f
#
#
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