In the previous message I forgot to mention:
When MET were modelled, there were no difference peaks anywhere. When I
changed them all to MSE, the large difference density peaks showed up.
Large *negative* difference density.
Hi CCP4ers,
I am looking for some advice on electrostatic maps of small molecules.
What is the best program for this?
Is there anyway I can calculate the desolvation energy at the same time?
I have tried to create a PQR file for APBS (through PDB2PQR) with the
pdb of the small molecule (and
Hello,
I am at a loss on what's going on:
I am refining SeMET containing structure and using REFMAC 5.2.0005 on Linux
and, the same thing happening, using REFMAC 5.5.0070 on Windows.
When MET were modelled, there were no difference peaks anywhere. When I
changed them all to MSE, the large di
When I "upgraded" to ibex it hosed my display, so this might not be of
much help, but in general,
1. You don't HAVE to use bash. You can use tcsh or zsh or any other
shell that suits your personal tastes. It just comes with a minimal
install to fit on a CD. Just issue
sudo apt-get inst
Sorry for typos. The " were replaced with ?
Victor
> Hi
Doing my first installation of CCP4 and also a Linux newbie, so try
to ?bear with me? ;-)
This message was sent using IMP, the Internet Messagin
*
*
*
Hi
Doing my first installation of CCP4 and also a Linux newbie, so try
to ?bear with me? ;-)
The ?install.sh? CCP4 script created a ?setup-scripts? directory,
with 2 shell subdirectories; ?csh? and ?sh?
In ?/home/victor/.bashrc? I found 2 lines:
sou
The latest version with all the bugfixes will of course appear in
CCP4-6.1.1. Until then, the latest binaries and source codes are
available on the mentioned webpage.
Pavol
Since version 5.5.0066 is the version in ccp4-6.1.0, is there going
to be a patch?
On Dec 19, 2008, at 12:32 PM, Jan Abendroth wrote:
Thanks a lot, Pavol,
that indeed did the trick.
refmacRwork Rfree RMSDb RMSDan
5.5.0063 0.1682 0.2118 0.0204 1.717
5.5.0066 0.1781 0.2247 0
Thanks a lot, Pavol,
that indeed did the trick.
refmacRwork Rfree RMSDb RMSDan
5.5.0063 0.1682 0.2118 0.0204 1.717
5.5.0066 0.1781 0.2247 0.0205 1.764
5.5.0070 0.1663 0.2102 0.0204 1.719
Cheers
Jan
On Dec 19, 2008, at 2:21 AM, Pavol Skubak wrote:
Hi Jan,
the difference
Dear all,
I have determined a structure with the resolution 2.0A and the spacegroup
P3121 from crystals grown at 4 degree. This apo-form structure is composed
of an N-terminal (a/b)8 TIM barrel (~300 AA) and two C-terminal domains
(~100 AA) which are named as Sub1 and Sub2. Meanwhile, I have als
On Dec 19, 2008, at 7:43 AM, Eric Liu wrote:
Hi All
Hi Eric:
I am a new user for OS X system and this question may sound naive. I
followed the instruction on website Crystallography on OS X,
installed X11,
Xcode and fink on my OS X 10.5.5, but still could not install ccp4
with
fink. He
Dear Eric,
A native installer for CCP4 6.1.0 for this platform is available from
the download web page:
http://www.ccp4.ac.uk/download/downloadman.php
this is a disk image and installs in the usual manner for macintosh
applications. This includes all of the components needed.
Best wishes,
Rajan,
have a look at http://www.imagenes-bio.de. I guess there are more
suppliers. Please send a summary to the board.
Good luck,
Guenter
Rajan Pillai wrote:
Hi All,
Apologies for a non-CCP4 question. I want to clone a couple of
proteins of human and mouse origin. Can anyone tell me where f
Hi All
I am a new user for OS X system and this question may sound naive. I
followed the instruction on website Crystallography on OS X, installed X11,
Xcode and fink on my OS X 10.5.5, but still could not install ccp4 with
fink. Here is the err message" no package found for specification "ccp4""
Yes, this is a bug. This is fixed now - you need 2 corrected ccp4i
files. See
http://www.ccp4.ac.uk/problems.php#6.1.0-sftools-interface
which has links to the fixed files.
Cheers
Martyn
On Thu, 2008-12-18 at 08:32 +, Winter, G (Graeme) wrote:
> Dear Engin,
>
> Yep, I can reproduce this usin
Alun,
There's only any point doing it if they're truly isomorphous (e.g. by
the Crick-Magdoff test), otherwise pairs of reflections with equal
indices won't sample the same points in the transforms, so you could
still end up with contamination.
Slow cooling or pseudo-MD such as randomly shifting
Hi Ian, Gerard,
Thanks for your replies.
Perhaps my hypothetical example wasn't a good one and may have clouded
the issue. Could I just confirm whether or not you think its necessary
to transfer initial free R assignment to any new data sets or to
isomorphous data sets such as substrate comp
Hi Jan,
the difference between 5.5.0063 and 5.5.0066 is just a few
bugfixes. However, unfortunately one of them introduced a
new bug to 5.5.0066 which has been fixed in the later
versions. Could you please upgrade to the latest version
(currently 5.5.0070) from
http://www.ysbl.york.ac.uk/~garib/re
Dear all,
I would like to inform you all of a vacancy we have for a Staff scientist
position
at the EMBL-Grenoble
http://www-db.embl.de/jss/servlet/de.embl.bk.emblGroups.JobsPage/08054.html
We currently looking for an experienced crystallographer at the EMBL-Grenoble
for
the mainentance, ro
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