with c axis reflections including 0,
0, l odd as well as even, which is sort of a hint here
From: MARTYN SYMMONS martainn_oshioma...@btinternet.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, 16 April 2013, 14:30
Subject: Re: [ccp4bb] Puzzling Structure
-written).
Cheers
Martyn
From: Michel Fodje michel.fo...@lightsource.ca
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, 15 April 2013, 17:19
Subject: Re: [ccp4bb] Puzzling Structure
Just to round up this topic, a bug report was submitted to PDBe concerning
entry
and 18 and tried to fix it by adding it back, between 1 and 8.
/Michel
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Edward A. Berry
Sent: April-14-13 9:59 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Puzzling Structure
Robbie Joosten wrote
On 15 Apr 2013, at 17:19, Michel Fodje michel.fo...@lightsource.ca wrote:
I imagine somebody accidentally deleted a space between P 21 21 2 and 18 and
tried to fix it by adding it back, between 1 and 8.
As this has now been mentioned twice in this discussion it should probably be
noted
: Friday, 12 April 2013, 22:57
Subject: Re: [ccp4bb] Puzzling Structure
Waters are moved during annotation using the perceived space group's
symmetry operation. So if the authors give the wrong space group,
then the annotation pipeline understandably messes things up. If the
originally
Hi Robbie,
Which seems a sort of reasonable attitude to me.
Not quite, the depositor has to give, i.e. type, the space group
what I don't get is why one needs to type in this information if it is
already present in both, model and data files? Any human typing is typo
prone. Ideally
Robbie Joosten wrote:
Hi Martyn,
I think the question is where the error was made - seeing the uploaded file
would clear this up. But it seems unlikely to me that the depositor saw a huge
R factor discrepancy at the end of refinement and just blithely uploaded it.
So scenario 3 :-
PDB : we
and making sure that the R you get is not twice as large as published one
would entirely suffice -:)
Pavel
From: Robbie Joosten robbie_joos...@hotmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Friday, 12 April 2013, 22:57
Subject: Re: [ccp4bb] Puzzling Structure
is not twice as large as
published one
would entirely suffice -:)
Pavel
From: Robbie Joosten robbie_joos...@hotmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Friday, 12 April 2013, 22:57
Subject: Re: [ccp4bb] Puzzling Structure
Waters are moved during
Has anyone else noticed a problem with the structure of the N-terminal capsid
domain of HIV-2 PDB 2wlv.
Load it up to in coot and navigate to residue B118.
/Michel.
By the way, you will need to show symmetry atoms to see the problem.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Michel Fodje
Sent: April-12-13 1:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Puzzling Structure
Has anyone else noticed
PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Puzzling Structure
By the way, you will need to show symmetry atoms to see the problem.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Michel Fodje
Sent: April-12-13 1:14 PM
To: CCP4BB
:
By the way, you will need to show symmetry atoms to see the problem.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Michel Fodje
Sent: April-12-13 1:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Puzzling Structure
Has anyone else noticed a problem
] on behalf of Michel
Fodje [michel.fo...@lightsource.ca]
Sent: Friday, April 12, 2013 2:17 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Puzzling Structure
By the way, you will need to show symmetry atoms to see the problem.
-Original Message-
From: CCP4 bulletin board
] Puzzling Structure
Has anyone else noticed a problem with the structure of the N-terminal
capsid domain of HIV-2 PDB 2wlv.
Load it up to in coot and navigate to residue B118.
/Michel.
The CRYST1 in the pdb header is problematic.
CRYST1 95.520 47.815 88.570 90.00 90.00 90.00 P 21 21 218
it looks like the number '1' was paired to the space group rather than the
space grop number (i.e. nr. 18 for P21212)
Table 1 in the paper specifies P212121 as the space group.
i meant to say P21212
On 12 Apr 2013, at 21:47, Savvas Savvides savvas.savvi...@ugent.be wrote:
The CRYST1 in the pdb header is problematic.
CRYST1 95.520 47.815 88.570 90.00 90.00 90.00 P 21 21 218
it looks like the number '1' was paired to the space group rather than the
/books/2008/9780854042722.asp
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Michel Fodje
[michel.fo...@lightsource.ca]
Sent: Friday, April 12, 2013 2:17 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Puzzling Structure
By the way
...@lightsource.ca
написал:
By the way, you will need to show symmetry atoms to see the problem.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Michel Fodje
Sent: April-12-13 1:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Puzzling Structure
Has
Of
Garib N Murshudov
Sent: Friday, April 12, 2013 21:39
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Puzzling Structure
It is typo:
R factor for p212121 - 0.4
for p21212- around 0.18
Although water seem to have been moved around using p212121
On 12 Apr 2013
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