Dear Sudarshan,
I have the feeling the your R factor after Molrep is really high because the
program has failed to produce a correct/not-partial solution, which could be
due to many things, but usually the main problem is how good your search model
is. The difference in spacegroups is not a pro
Hi Fellows,
I have bugged now the ultimate authorities including Howard Flack (of Flack
parameter fame),
and alas, there is no official descriptive adjective for these 65 Söhnke space
groups.
Chiral is definitely wrong, and so is enantiomorphic, although 22 of the
nameless form 11
enantiomo
We need more information.
First if the pointgroup is hexagonal are you searching al likely SPACEgroup
- eg PG P6, SGs might P6 P61 P62P63 P64 P65..
There is a GUI option to do this for both MOLREP & Phaser.
You can guess the likely no of molecules using matthews
In the GUI - that is in the MOL RE
Hi Tim,
What can be a reason to work with an obsolete version of CCP4?
I remember reading somewhere that 6.3.0 version is obsolete.
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular
Microbiology and Biotechnology
Tel Aviv University 69978, Israel
A
Hi Felix
You're very trusting! Bugs in new versions of software are not unknown!
The bug may not manifest itself in a program crash (though it makes life
easier if it does), rather it may simply give different numerical results
that you may not spot for some after. This is why CCP4 distributes t
Dear all,
I am looking for a software solution to organize many pieces of information
1.) Results from (bio)chemical experiments, such as spectral data, pictures.
2.) Project ideas, milestones, etc.
3.) Literature, including tags, short comments, etc.
For example, for a certain project I would
Dear Sudarshan,
There are quite a few point to consider in MR:
-How good is your model? At >50% sequence identity with your protein, it is
probably ok, around 25% sequence identity it may or may not work. If your
protein is of the same protein family with a similar biological function it is
pro
On Mon, Apr 28, 2014 at 03:51:57PM +0100, Ian Tickle wrote:
> Harry,
>
> I've run into this problem before with other programs when I switch between
> v6.3 & v6.4. I think the problem is this code in ccp4.setup-sh:
>
> if [ `expr ":${PATH}:" : ".*:${dir}:"` -eq 0 ]; then
We can remove this co
Hi Marcin
It was obviously added originally because there was a limit to the length
of the PATH variable (presumably there still is), so repeated invocations
of setup scripts could take you over the limit. Ideally the script should
remove old versions from the PATH, not just prepend the new one,
Hi Ian,
Improving the CCP4 tests is a priority. We (the core team) have a project
looking into that. If developers have their own tests for components of the
suite that have not made it into the distribution, then we'd be happy to
collect them for the new test set.
Best wishes
-- David
On 29 A
Dear All,
A 4-year BBSRC DTP PhD (1 year MRes and 3 year PhD) position is available in my
lab jointy supervised with Dr Ed Tate (Department of Chemistry) at Imperial
College London. The project involves structure based inhibitor design for
multi-drug bacterial membrane transporters. The PhD will
The Helmholtz Zentrum Berlin für Materialien und Energie, the
Max-Delbrück-Center for Molecular Medicine Berlin, the Freie Universität
Berlin, the Humboldt Universität zu Berlin and the Leibniz-Institute for
Molecular Pharmacology jointly operate three experimental stations for
bio-macromole
Response to off-board mail:
>How about [calling them] non-centro-symmetric space groups, as I often tell my
>students?
Almost, but not exact enough.
The 65 are only a subset of non-centrosymmetric space groups:
Not all enantiogenic (not elements of the 65-set) space groups are
centrosymm
Bernhard
The term "enantiomorphic pair" is used consistently in ITC-A to mean one of
the 11 pairs of what you previously called "chiral space groups".
PersonalIy I would never use the term "chiral" in this context even though
it is synonymous with "enantiomorphic" (I would reserved "chiral" for
si
Here’s a summary of options people have sent me and some other related info I
found on my own (email traffic has slowed down, so assuming all votes are in):
-Inteins: cut themselves off/out in presence of DTT or similar. NEB sells kits.
-Sortase-His6: like inteins, but activated by Ca++ or trig
Dear Tobias,
My group uses a web based content management system called drupal to manage
inventory, orders and are now setting it up to manage data. Drupal has a
SQL server to manage different types of information and it is normally
utilized to build websites, but you can also use it as a databas
Hi Tobias,
There is Quartzy, which is free.
https://www.quartzy.com
I am not sure it covers all of your desired functionalities.
Best regards,
Florian
On Apr 29, 2014, at 7:21 AM, Tobias Beck wrote:
> Dear all,
>
> I am looking for a software solution to organize many pieces of information
Dear colleagues:
We have a position available for an X-ray crystallographer. The job
description follows. If you have any questions, please feel free to contact me.
Investigator III, Structural and Biophysical Chemistry
About Novartis Institutes for Biomedical Research:
At Novartis Institutes
Summary: CASP is soliciting target proteins for structure prediction -
specifically proteins with new folds, membrane proteins, disordered proteins,
oligomers, complexes, and multi-domain proteins.
Call for targets:
=
As many of you know, CASP (Critical Assessment of Structure Pred
Wishing you all the best Jason, it has been fantastic to be involved with this
bb with you as the key guy. Always there to answer the questions
From: Jason Vertrees [mailto:jason.vertr...@gmail.com]
Sent: Thursday, 24 April 2014 9:00 p.m.
To: pymol-users; ccp4bb@jiscmail.ac.uk
Subject: [PyMOL] Fa
Hi,
I have shelx programs installed on my computer but only shelxs shows as active
on the ccp4i interface. How to activate shelxCDE?
Thanks,
Mirek
Dear Bernhard (and others),
I was looking for catchy combinations of "chiral" or "enantio" and
Latin or Greek words for "support" or "allow" -- until I realized there
is already a name for this very concept, used widely in chemistry:
I think the precise and correct term applicable to the "65"
actually, I'll have to amend that:
> Dear Bernhard (and others),
> I was looking for catchy combinations of "chiral" or "enantio" and
> Latin or Greek words for "support" or "allow" -- until I realized there
> is already a name for this very concept, used widely in chemistry:
> I think the pre
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