Dear CCP4 Users
An update for the CCP4-6.4.0 series has just been released, consisting
of the following changes
• refmac5 (all platforms):
– Fixed restraints for M- and P-peptides
– Fixed SAD scaling issue
• monomers (all):
– Fixed description for M- and P-peptides and some other entries
On 13/06/14 11:39, Alexander Schuettelkopf wrote:
On 13/06/2014 03:43, Paul Emsley wrote:
On 13/06/14 00:19, Ethan A Merritt wrote:
This is a known problem with cprodrg - no need to report it. Cprodrg
will undergo little to no maintainance from now on.
Well, it was not known to me. While ther
To all who might be interested
We are seeking a full-time Research Technician to work at the Membrane Protein
Laboratory (MPL) located at the Diamond Light Source in Oxfordshire.
The MPL at Diamond Light Source is a Wellcome Trust funded facility created in
collaboration between Imperial College
On Friday, 13 June 2014 10:12:50 AM Tim Gruene wrote:
> Hi Ethan,
>
> Maybe I miss something, but whenever an error in one of the cif-files
> has been reported, be it directly to Garib, or publicly on the ccp4bb,
> Garib (I assume) fixed very quickly - I don't quite understand why we
> need a new
To all who may be interested.
Neil McDonald has asked me to forward this message to the bulletin
board. Please reply to him at neil.mcdon...@cancer.org.uk and NOT to me.
Thanks
Andrew
=
Postdoctoral Position (4 years), Str
Do those fixes also make it to the phenix version of the library? Yes,
this is the CCP4bb, but the monomer library is also used by Phenix, and
a good number of structures (almost half of those deposited this year?)
in the PDB now come from phenix.refine. Or in other words, is there a
central, h
Dear all,
As I did give the full promotional message for why these are just outstanding
meetings to attend, I will only invite you to
look at the latest programs
GRC (http://www.grc.org/programs.aspx?id=11654)
GRS (http://www.grc.org/programs.aspx?year=2014&program=grs_diff).
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Hi Robbie,
Frank probably meant the status of the model when the author is ready
for deposition, i.e., already after additional refinement.
The B-factor assumes a harmonic oscillation of its atom on a linear
trajectory (maybe the superposition of one
Hi Tim,
The decision of which atoms you can and cannot see in your map is rather
subjective. Also the way you generate your map can make a big (enough)
difference. A new map after additional refinement, an NCS averaged map, or a
feature-enhanced map might show you the position of (some of) the
Hi Tim,
The problem I see with including atoms with no density is that the one
place you can guarantee those atoms are not (at 100% occupancy), is at the
coordinates assigned to them.
I would argue that the scientific inaccuracy of such a model should
outweigh the desire to use the coordinates for
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Hi Robbie,
maybe it is good not to use coordinates for calculations if you cannot
measure the coordinates?
Cheers,
Tim
On 06/13/2014 12:35 PM, Robbie Joosten wrote:
> Hi Tim,
>
> The problem with missing atoms in ligands is that you cannot use
> th
What version of Aimless are you running? I thought I had fixed that bug
Phil
On 13 Jun 2014, at 11:59, Andreas Förster wrote:
> Dear all,
>
> I'm trying to scale/merge mtz files in ccp4
> (Pointless/Aimless/ctruncate/Rfree pipeline) and keep getting an
>
> UNHANDLED EXCEPTION: vector::_M_ran
Dear all,
I'm trying to scale/merge mtz files in ccp4
(Pointless/Aimless/ctruncate/Rfree pipeline) and keep getting an
UNHANDLED EXCEPTION: vector::_M_range_check
at the end of the aimless step, right after the standard deviation v.
intensity tables. The output mtz file is not written and c
On 13/06/2014 03:43, Paul Emsley wrote:
> On 13/06/14 00:19, Ethan A Merritt wrote:
>
>
> This is a known problem with cprodrg - no need to report it. Cprodrg
> will undergo little to no maintainance from now on.
Well, it was not known to me. While there is indeed little active
development at t
Solubility issues though?
Dr David C Briggs PhD
http://about.me/david_briggs
On 13 Jun 2014 11:45, "Ian Clifton" wrote:
> avinash singh writes:
>
> > wwdwwwy
>
> Wow, imagine the fluorescence from that…
>
> --
> Ian ◎
>
avinash singh writes:
> wwdwwwy
Wow, imagine the fluorescence from that…
--
Ian ◎
wwdwwwy
Hi Tim,
The problem with missing atoms in ligands is that you cannot use the
coordinates for any follow-up calculation that requires ligand topology (e.g.
restraint generation). That forces you to rely on the annotation of the
compound, for instance at the PDB. That can be quite messy and leave
Dear CCP4ers,
We would like to remind you that the registration for this workshop,
that will take place in very nice surroundings in Oeiras (Portugal)
next October 10-12, is still open.
The Workshop will divided into 5 sessions covering the following topics:
- Structural Biology
- Chromatin
Hi Frank,
I agree with what Tim has just posted.
Personally I would not think occupancy=0, since this would mean the atom is
not where you placed it (i.e. nowhere near). This could be useful if all
your ligand has the same partial occupancy or, if you have multiple poses,
the sum of occupancies of
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Hi Frank,
if you can calculate their position, i.e. it is part of a rigid group,
I would leave it. If it is flexible, I would remove it because the
reader of my deposited structure may not be a crystallographer and
misinterpret the result.
If it is o
Hi all - talking about ligands, a quick question on that old conundrum,
of what to do about invisible atoms -- build them with occ=0, or omit them?
For bits of protein, I know all the arguments; personally I prefer
omitting atoms because:
* for amino acid sidechains, their presence is impli
Dear Ethan,
Alexander Schuettelkopf has sent us modified PRODRG parameter file to fix
this issue. We'll distribute it in CCP4 updates soon.
If you'd like to test it now, the prodrg.param file is here:
http://fg.oisin.rc-harwell.ac.uk/scm/loggerhead/cprodrg/trunk/download/head:/prodrg.param-2012100
A postdoctoral position is available immediately on structural studies of
protein-protein interactions at the core of the human Hedgehog signaling
pathway, as part of a long-term collaboration between the laboratories of Rune
Toftgård and Luca Jovine at the Department of Biosciences and Nutritio
Hi Ethan,
Maybe I miss something, but whenever an error in one of the cif-files
has been reported, be it directly to Garib, or publicly on the ccp4bb,
Garib (I assume) fixed very quickly - I don't quite understand why we
need a new term for this process?
Best,
Tim
On 06/12/2014 10:45 PM, Ethan A
I sense someone should quickly point out, on behalf of the developers (I
assume it's they that are requested to magically "give optimal
support"), that it's not for want of awareness, intelligence or
diligence that this functions are suboptimal: it's want of TIME. As
Paul suggested, in ccp4 a
Dear Appu,
If it is possible to solve your structure with currently available MR models
using any currently existing technology, one of these programs will be able to
do it. Throwing yet another program at the problem won’t help, especially an
older program that was good in its time (and is st
Dear Ruby,
They are a dedicated beam line for Biological Sample at the ESRF (BM29);
informations are here:
http://www.esrf.eu/UsersAndScience/Experiments/MX/About_our_beamlines/BM29
and scheme to apply is here:
http://www.esrf.eu/UsersAndScience/UserGuide/Applying/ProposalGuidelines/MXnon-BA
Hei Tom,
We may not be able to prevent deposition of dodgy structures, but we could at
least give optimal support to those of us wanting to do a good job. With
respect to ligands, the support could sometimes be better - thinking in
particular of carbohydrate ligands.
Best,
Ute
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