parametrised.
Cheers
Joel
-Original Message- From: CCP4 bulletin board
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie Joosten Sent:
Thursday, 12 July 2012 12:16 a.m. To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Chiral volume outliers SO4
Hi Ian,
@Ian: You'd be surprised how well
On Sunday, 15 July 2012, Dale Tronrud wrote:
There are good reasons for maintaining order in this human-induced
numbering scheme. A common operation is to superimpose two molecules
and calculate the rmsd of the positional differences. This calculation
is not useful when the Val CG1 and
board
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie Joosten Sent:
Thursday, 12 July 2012 12:16 a.m. To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Chiral volume outliers SO4
Hi Ian,
@Ian: You'd be surprised how well Refmac can flatten sulfates
if you have a chiral volume outlier (see
would allow you to distort the molecule.
Cheers,
Robbie
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Tim Gruene
Sent: Friday, July 13, 2012 10:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Chiral volume outliers SO4
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Dear Robbie and ccp4bb,
Is 1N1 not a different type of problem though, where a chirality
restraint is valid and so the atom labelling is important?
Are you saying that we should always use the cif dictionary, even when
there are errors? Surely in the SO4 case, as Ian said, it is better to
...@mail.cryst.bbk.ac.uk]
Sent: Friday, July 13, 2012 14:09
To: Robbie Joosten
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Chiral volume outliers SO4
Dear Robbie and ccp4bb,
Is 1N1 not a different type of problem though, where a chirality restraint
is
valid and so the atom labelling
@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Chiral volume outliers SO4
Hi Andrew,
Indeed, provided the atom labeling is correct the chiral volume restraint
actually says whether the groups on the ring a axial or equatorial. The cif
files do not define that any other way, so without the restraint
July 2012 12:16 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Chiral volume outliers SO4
Hi Ian,
@Ian: You'd be surprised how well Refmac can flatten sulfates if you
have a chiral volume outlier (see Figure 1d in Acta Cryst. D68:
484-496
(2012)).
But this is only because
July 2012 12:16 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Chiral volume outliers SO4
Hi Ian,
@Ian: You'd be surprised how well Refmac can flatten sulfates if you
have a chiral volume outlier (see Figure 1d in Acta Cryst. D68:
484-496
(2012)).
But this is only because
.
I'll look at swapping the oxygens in the SO4's.
Cheers
Joel
-Original Message-
From: Dale Tronrud [mailto:det...@uoxray.uoregon.edu]
Sent: Friday, 13 July 2012 10:22 a.m.
To: Joel Tyndall
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Chiral volume outliers SO4
While this change has
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Hash: SHA1
Dear Joel,
out of curiosity: what is the Chiral volume outliers issue?
Cheers,
Tim
On 07/11/12 01:00, Joel Tyndall wrote:
Hi people,
We are refining a structure with sulfates and we are getting the
Chiral volume outliers issue. I understand
Well - the problem may well be here - in the REFMAC dictionary (see
$CLIBD/monomers.s.SO4.cif ) the chiral volume calculation uses at the order
of the O numbering around the S atom .
So if your O numbering is not right handed you will have the chiral volume
calculated as positive, not negative.
: [ccp4bb] Chiral volume outliers SO4
Well - the problem may well be here - in the REFMAC dictionary (see
$CLIBD/monomers.s.SO4.cif ) the chiral volume calculation uses at the order
of the O numbering around the S atom .
So if your O numbering is not right handed you will have the chiral volume
Cryst. D68:
484-496 (2012)).
Cheers,
Robbie
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf
Of Eleanor Dodson Sent: Wednesday, July 11, 2012 12:15 To:
CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Chiral volume outliers
SO4
Well - the problem may well
On 11 July 2012 11:39, Robbie Joosten robbie_joos...@hotmail.com wrote:
@Ian: You’d be surprised how well Refmac can flatten sulfates if you have a
chiral volume outlier (see Figure 1d in Acta Cryst. D68: 484-496 (2012)).
But this is only because the 'negative' volume sign was erroneously
used
Hi Ian,
@Ian: You'd be surprised how well Refmac can flatten sulfates if you
have a chiral volume outlier (see Figure 1d in Acta Cryst. D68: 484-496
(2012)).
But this is only because the 'negative' volume sign was erroneously used
in
the chiral restraint instead of 'both' (or better
Hi people,
We are refining a structure with sulfates and we are getting the Chiral volume
outliers issue. I understand the problem as being computational where the
oxygens are in reality equivalent but computationally named differently. I have
seen the recent Acta Cryst D paper (April 2012 -
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