Dear CCP4 Community,
our laboratory is going to dismantle an in-house X-ray diffraction
instrumentation. It consists of a Rigaku RU-200 rotating anode, an
Osmic Blue confocal system, a RaxisIV++ detector, and an Oxford
cryostream cooling device. All instruments have been properly
maintained and ar
Alternatives to ChemDraw 3D? Yes, ChemDoodle!
I installed XDrawChem on Mac OSX 10.4.11 but it crashes all the time
which is somewhat annoying.
Then I finally stumbled upon ChemDoodle *which is not for free* but the
trial version solved my problem at that time.
Having worked with it, I really
Dear All,
Is there a way to transform a cell in Pymol? I want to superimpose cells
of my two crystal forms, when I use the align command, molecule from one
unit cell transforms on to other, but the cell stays the same. I just
want to look if by any chance my cells of two different crystal form
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Yes, thanks! I wish I had spotted that before!
As you say Tables 2.2.3.2 (pp 212-213 in my ed.) & 2.2.3.4 (pp 214-215),
for non-centrosymmetric primitive & centred space groups respectively,
contain all the authoritative information you need to define the allowed
origin shifts (as well as info on
Hi there,
I am refining a 1.3AA structure for SSGCID using
--
Jan Abendroth
Emerald BioStructures
Seattle / Bainbridge Island WA, USA
home: Jan.Abendroth_at_gmail.com
work: JAbendroth_at_embios.com
http://www.emeraldbiostructures.com
Hi all,
I am trying to use the transform map command in coot but i am getting the
following error
6:19: In expression (0.9956 -0.08709 -0.03537 ...)::6:19: Wrong type to
apply: 0.9956
the command that i used was:
(transform-map 13 (0.9956 -0.08709 -0.03537 -0.08702 -0.9962 0.003531
-0.03554 -0.00
I think the space-group and cell are missing:
It should be something like:
(transform-map imol rotation-matrix trans point radius space-group cell)
i.e. in your example, say:
(transform-map 13 (list 0.9956 -0.08709 -0.03537 -0.08702 -0.9962
0.003531
-0.03554 -0.0004371 -0.9994) (list 1.235 1.005 0
Hi there,
apologies for the previous email, hit the send button too early.
Hope everyone could stand the suspense for the continuation of the story ;-)
Here we go:
I am refining a 1.3AA structure for SSGCID using refmac5.5.102 or 109, OSX.
A typical grey zone case for anisotropic refinement, yet i
Rana Refaey wrote:
Hi all,
I am trying to use the transform map command in coot but i am getting the
following error
6:19: In expression (0.9956 -0.08709 -0.03537 ...)::6:19: Wrong type to
apply: 0.9956
the command that i used was:
(transform-map 13 (0.9956 -0.08709 -0.03537 -0.08702 -0.9962 0.
Dear Ian,
Although these tables are indeed very useful, on closer perusal I have
found a typo in my edition (which appears to be the same as yours but
slightly different to the on-line edition) - in the 3rd column of table
2.2.3.2, "P6" should obviously have a bar over the "6", though this is
un
Sixth International Workshop on X-ray Radiation Damage to Biological
Crystalline Samples
To be held at the Stanford Synchrtron Radiation Laboratory from
13:00 March 11th to 13:00 March 13th 2010.
Registration and Abstract submission is now open and can be found at:
http://www-conf.slac.stanford.e
Hi all,
I use fink to install ccp4-6.1.2 on my Mac OS X 10.6. All programs in ccp4
works well except imosflm. when I run it, it gives me the following error
message"
Top level CCP4 directory is /sw64/share/xtal/ccp4-6.1.2
Using CCP4 programs from /sw64/share/xtal/ccp4-6.1.2/bin
MOSDIR is /Use
Hi George, Ian,
I have attached a script that computes the alternative origins for a
given space group (or all of them) using procedures outlined by Ralf
(Acta Cryst. 1999, A55, 383-395).
Run it with phenix.python origins.py
For R3 and R32 in both rhombohedral and hexagonal setting we get
R3
Hi all,
I have installed coot 0.6.1 in my Mac OS X 10.6. But the Prove chashes
button in validate is grey.
How to get 'Probe clashes" work in coot?
Thank you very much!
yamei
The easiest thing to do is:
export MOSFLM_WISH=/usr/bin/wish8.4
or
fink install imosflm-aqua
will make sure everything is set up ok for 10.6, where the supplied aqua
TclTK plays well with imosflm.
Yamei Yu wrote:
> Hi all,
>
> I use fink to install ccp4-6.1.2 on my Mac OS X 10.6. All progr
This is available to install as a binary from here:
http://molprobity.biochem.duke.edu/get_molprobity.php
Although probe and MolProbity3 are said to be "free and open source software
distributed under a BSD-style license", I can't find the source code, so I
can't make coot depend on it within
On Mon, Feb 8, 2010 at 1:51 PM, William G. Scott wrote:
> This is available to install as a binary from here:
>
> http://molprobity.biochem.duke.edu/get_molprobity.php
>
>
> Although probe and MolProbity3 are said to be "free and open source
> software distributed under a BSD-style license", I ca
This may be somewhat convoluted but for this exact purpose try ZINC.
For other drawing things then yes use one of the other packages
http://zinc.docking.org/
Draw the molecule using the widget, save the smiles file and let their
server make the 3D version for you, properly protonated etc. A
On Feb 8, 2010, at 2:07 PM, Nathaniel Echols wrote:
> On Mon, Feb 8, 2010 at 1:51 PM, William G. Scott > wrote:
>
>> This is available to install as a binary from here:
>>
>> http://molprobity.biochem.duke.edu/get_molprobity.php
>>
>>
>> Although probe and MolProbity3 are said to be "free and
There are several more options to create 3D coordinates from it's 2D
drawing:
You can build any 3D molecule easily in Discovery Studio Visualizer -
It is free but not for Mac OS
there is nice server called Frog, that convert 2D to 3D and can
build set of conformers http://bioserv.rpbs
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