Although Zby's remarks re precision are beyond my original bewilderment
about listed zepto-meter range digits (sans precision measure),
I wonder whether the argument that we have so many data and thus a quite
high precision (n.b. not accuracy) can be attained,
is perhaps somewhat optimistic. What
Hi Fellows,
something that may eventually become an issue for validation and reporting
in PDB headers:
using the Refmac grouped occupancy keyword I was able to form and refine
various networks of correlated
alternate conformations - it seems to works really well at least in a 1.6
and 1.2
Hi Bernhard,
The validation of alternates is indeed quite poor and any improvements would
probably depend on proper annotation by the depositor, particularly in complex
correlated cases.
For your model I would probably make the two waters alternates of each other.
That way, it is easier to
Dear Tarek
There are several things to consider:
1-At an MX beamline the X-ray fluorescence (XRF) scans are usually used
to define good energies for measurement of anomalous data.
While XANES and XRF in general are similar techniques, they are used for
very different applications. This said,
Dear Atul,
I suggest to run SDS-PAGE with your crystals. You can even use
micro-crystalline precipitate that you probably have from optimization
stage. May be protein dissociated into subunits in the crystallization
conditions. But I am not sure because I know nothing about your protein.
As far as the *ICCBM15 pre-conference workshop* is concerned (consisting
of short presentations, practical demonstrations and hands-on exercises
taught by an international team of experts), the workshop is already
completely overbooked.
Students, postdocs and scientists interested in the
Dear CCP4 Users
An update for the CCP4-6.4.0 series has just been released, consisting
of the following changes
• crank:
– bug fix in bp3
– update to overcome OMP problem
• ctruncate:
– update to 1.15.9
• aimless:
– update to 0.3.7
• pointless:
– update to 1.9.11
– fix for
I would probably make the two waters alternates of each other.
Quite possible, but the group definition, i.e. to which alt conf. side chain
they belong,
would need to be preserved, too.
BR
Cheers,
Robbie
Sent from my Windows Phone
_
Van: Bernhard Rupp
Verzonden:
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Hi Bernhard,
do you refer to the PDB who, according to Martyn, remove the altloc
indicator? That's certainly a serious bug that should be fixed as
quickly as possible.
Within refmac the preservation is fine and as you would expect it to
be: altA
?? Refmac knows because of the group definition, otherwise I cannot force
grouped occupancy refinement.
There is no definition in PDB that eg ALTLOC A (of whatever residue) belongs to
ALTLOC A of (whatever) residue/water.
BR
-Original Message-
From: Tim Gruene
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Hi Bernhard,
That's right, the definition is not in the PDB, but REFMAC sensibly
handles it this way. It is certainly a short-coming if not bug in the
PDB (definition).
Best,
Tim
On 07/23/2014 04:49 PM, Bernhard Rupp wrote:
?? Refmac knows because
I agree that it would be excellent to be able to associate
alternate conformations (beyond the individual residue) but
when we defined the PDB format we had an 80-column limitation
per atom and so only one column was allowed for alternate
conformations. In an ASCII world only 36 characters were
On Wed, Jul 23, 2014 at 3:25 AM, MARTYN SYMMONS
martainn_oshioma...@btinternet.com wrote:
The practice at the PDB after deposition used to be to remove water
alternate position indicators - although obviously to keep their partial
occupancies.
This has not been my experience - see for
One could check if the alternate conformations are part of a continuous
alternate zone or if they make contact (no contact, no association). However, I
think it is time to abandon the PDB format and move to cif or some other format.
My 2 cents,
Herman
-Ursprüngliche Nachricht-
Von:
An additional problem is existence of alternative conformations close to
rotational axis that violate crystal symmetry.
If we want to describe such correlated alternative configurations, we need
to describe also how they transform by such rotational axis.
This problems may also exists also for
Dear Colleagues,
Stimulated by Bernhard's posting, and whilst certainly beyond his sense of
bewilderment, I recalled that there were studies on this issue. These are
neatly summarised in the Topical review :-
http://dx.doi.org/10.1107/S01087681269X
By Frank Herbstein in Acta Cryst B
I
I think there has been historically some glitch in the deposition of some
refmac altloc waters
So for example 4a9x from Buster is annotated correctly
REMARK 3 PROGRAM : BUSTER 2.11.2
HETATM 9407 O HOH A2517 -22.429 1.144 -35.218 1.00 29.73 O
HETATM 9408 O AHOH
Where is it written that compactness of representation and
accuracy/precision are the same thing? Is 1/3 more or less precise than
0.333 ?
If mmCIF were a binary floating-point format file, there would be more
decimal places in the precision of the stored value for the unit cell,
despite
Dear Frances,
I don't think that you can put the blame entirely on the 80 column
limitation.
The program SHELX76 was limited to 80 columns because the input came as
punched cards. It introduced a simple concept, the /free variables/,
that are frequently used to represent occupancies and can
The representation is simply non-parsimonious. There is no meaning to
the zepto-meter digits.
Numquam ponenda est pluralitas sine necessitate.
BR
From: James Holton [mailto:jmhol...@lbl.gov]
Sent: Wednesday, July 23, 2014 9:58 PM
To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK
Subject:
An ad hoc kludge that is admittedly undesirable but at least does not break
anything
with the PDB format could be as was done e.g. with the TLS and NCS records -
put the alternate
group definitions into a REMARK record...
Best, BR
-Original Message-
From: CCP4 bulletin board
Greetings all -
My interest in the rest of the discussion of experimental precision and error
notwithstanding, and at the risk of stating explicitly what some might consider
obvious, it seems to me that no one has actually (intentionally) asserted that
they have determined the unit cell to
Post-doctoral position in Singapore at the Duke-NUS is
available
A post-doctoral position is available at the laboratory of Shee-Mei
Lok (http://www.loksheemeilab.com) in the emerging infectious disease program
of the Duke-NUS. Duke-NUS graduate medical school situated in Singapore, is a
global
Hello,
A solution exists also for PDB records:
As a consequence of a discussion with George which took place years ago, I
have taken the liberty to extend the PDB record length of 80 characters and
use additional characters to specify the group ID and their members list number
and provided
Hi all,
I’m trying to install a copy of moleman2 for my new Mac. (the version is
10.9.3). while I copy the osx_moleman2 from xutil directory I got the
following message: The Finder can’t complete the operation because some data in
“osx_moleman2” can’t be read or written.
(Error code -36)
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