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
select out one of the two alternate conformations.
Cheers,
Robbie
Sent from my Windows Phone
Van: Bernhard Rupp
Verzonden: 23-7-2014 10:19
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] correlated alternate confs - validation?
Hi Fellows,
something that may
nates of each other.
That way, it is easier to select out one of the two alternate conformations.
Cheers,
Robbie
Sent from my Windows Phone
Van:
Bernhard Rupp
Verzonden:
23-7-2014 10:19
Aan:
CCP4BB@JISCMAIL.AC.UK
Onderwerp:
[ccp4bb] correlated alternate confs - validation?
Hi Fellows,
somet
3-7-2014 10:19
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] correlated alternate confs - validation?
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
vari
nhard Rupp Verzonden: 23-7-2014 10:19 Aan:
> CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate
> confs - validation?
>
> Hi Fellows,
>
>
>
> something that may eventually become an issue for validation and
> reporting in PDB headers:
>
>
>
&
-ac.gwdg.de]
Sent: Mittwoch, 23. Juli 2014 15:38
To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] correlated alternate confs - validation?
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi Bernhard,
do you refer to the PDB who, according to Martyn, remove the altloc indicator
mailto:t...@shelx.uni-ac.gwdg.de] Sent: Mittwoch, 23. Juli 2014
> 15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re:
> [ccp4bb] correlated alternate confs - validation?
>
> Hi Bernhard,
>
> do you refer to the PDB who, according to Martyn, remove the altloc
>
L.AC.UK Subject: Re:
[ccp4bb] correlated alternate confs - validation?
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 w
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
up 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: 23-7-2014 10
program authors.
all the best
Martyn
Martyn Symmons
Cambridge
Original message
>From : f...@bernstein-plus-sons.com
Date : 23/07/2014 - 16:20 (GMTDT)
To : CCP4BB@JISCMAIL.AC.UK
Subject : Re: [ccp4bb] correlated alternate confs - validation?
I agree that it would be excellent to be a
twoch, 23. Juli 2014
15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re:
[ccp4bb] correlated alternate confs - validation?
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
qui
Just a quick thought that might be a workaround solution within the PDB format
restrictions: In NMR structures there are often multiple conformations stored
in different MODEL sections - this should in principle be possible for x-ray
structures as well, shouldn't it?
Of course this is a waste o
As an additional comment on the issue of spatially correlated disorder,
SHELX (and possibly other programs) has an elegant way of handling bump
generation between disordered atoms. SHELX will only generate a bump if
two atoms are in van der Waals conflict AND their occupancies sum to 1.1
or greate
: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Frances
C. Bernstein
Gesendet: Mittwoch, 23. Juli 2014 17:20
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] correlated alternate confs - validation?
I agree that it would be excellent to be able to associate alternate
conformations
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
herman.schreu...@sanofi.com
Sent: Wednesday, July 23, 2014 5:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [ccp4bb] correlated alternate confs - validation?
One could check if the alternate conformations are part of a continuous
alternate zone or if they
gt; Betreff: Re: [ccp4bb] correlated alternate confs - validation?
>
> 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 o
alf Of dusan
turk
Sent: Donnerstag, 24. Juli 2014 05:32
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs -
validation?
Hello,
A solution exists also for PDB records:
As a consequence of a discussion with George which took place years ago, I
have
st, BR
>
>
>
>
>
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf
> Of dusan turk Sent: Donnerstag, 24. Juli 2014 05:32 To:
> CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Betreff: Re: [ccp4bb]
> correlated alternate confs - validation?
>
>
>
kludges probably won't do.
BR
-Original Message-
From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de]
Sent: Donnerstag, 24. Juli 2014 12:10
To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs -
validation?
-
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