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)
Could
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
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global p
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 10^-
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 [mailto:C
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: Re:
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
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
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
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 ima
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 ot
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: CCP
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
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
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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
?? 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 [mailto:t...@shelx.uni-ac.
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
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 only
>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: 23-7-
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 inconsis
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 lat
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.
Also,
The practice at the PDB after deposition used to be to remove water alternate
position indicators - although obviously to keep their partial occupancies. I
think this was an 'undocumented feature' of the old annotation system. The new
mmCif-based annotation methods may be more adaptable.
I thi
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,
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 sele
Dear CCP4ers,
also in my experience, processing the same raw images with different
programs results in unit cell constants that typically deviate at least
already in the first digit after the dot (if not before the dot), with
our usual unit cell lengths between, say, 50-350 A. This leads to a
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
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 w
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