, BR
For every sufficiently complex problem there is an answer that is simple, clear
and wrong.
LH Mencken
From: Narayan Viswam [mailto:nvisw...@gmail.com]
Sent: Monday, April 27, 2015 12:02 PM
To: b...@hofkristallamt.org
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] 3BDN, 16.5
.
Regards,
Vaheh Oganesyan
www.medimmune.com
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie
Joosten
Sent: Friday, April 24, 2015 2:37 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!
The PDB_REDO entry for 3bdn was pretty old, so I
: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!
Hi Robbie and Co,
These things are happening now too. Look at the entry 4x4m. The paper got
published in January, PDB released coordinates in April. That means reviewers
did not have a chance to look even at validation report. In my opinion
,/
/ /
/Vaheh Oganesyan/
/www.medimmune.com/
*From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On
Behalf Of *Robbie Joosten *Sent:* Friday, April 24, 2015 2:37 AM
*To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] 3BDN, 16.5%
Ramachandran Outliers!
The PDB_REDO entry
*To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] 3BDN, 16.5%
Ramachandran Outliers!
The PDB_REDO entry for 3bdn was pretty old, so I replaced it using
a newer version of PDB_REDO that can use nucleic acid restraints
from LibG: http://www.cmbi.ru.nl/pdb_redo/bd/3bdn/index.html.
Obviously
with specific entries, feedback is always welcomed. We might be able
to solve the problem and improve out software in the process.
Cheers,
Robbie
Date: Thu, 23 Apr 2015 16:15:41 -0700
From: wgsc...@ucsc.edu
Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!
To: CCP4BB@JISCMAIL.AC.UK
.
--
*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
Oganesyan, Vaheh [oganesy...@medimmune.com]
*Sent:* Monday, April 27, 2015 9:04 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!
Hi Robbie and Co
---
*From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
*Misbah
ud Din Ahmad
*Sent:* Thursday, April 23, 2015 2:05 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!
I feel rather
. To bad that came at the expense of the
crystallography.
Cheers,
Robbie
Date: Thu, 23 Apr 2015 18:43:13 +
From: kell...@janelia.hhmi.org
Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!
To: CCP4BB@JISCMAIL.AC.UK
Is it in pdb redo? Take a look here:
http://www.cmbi.ru.nl
Dear crystallographers,
The PDB entry
http://www.rcsb.org/pdb/explore.do?structureId=3BDN
has 16.5% Ramachandran outliers. When I opened this PDB file in coot and
checked for Ramachandran outliers, the results are:
In preffered region: 58.04%
In allowed regions: 19.78%
*Outliers: 22.17%
Dear Mishba,
Just check density vs model by simply open 'Coot',
Go to: 'File' - 'Fetch PDB Map using EDS'
Type the pdb entry into the field - enjoy the densities.
Best and god save the EDS,
Gert
-
LOEWE Center for Synthetic Microbiology
It was published in Nature so it must be right :) ...
Dear crystallographers,
The PDB entry
http://www.rcsb.org/pdb/explore.do?structureId=3BDNhttp://www.rcsb.org/pdb/explore.do?structureId=3BDN
has 16.5% Ramachandran outliers. When I opened this PDB file in coot
and checked for
Dear Gert,
I just did that and I wonder how these structures end there !!!
@ Sabine: I was talking about Ramachandran outliers. I had learnt that the
number of Ramachandran outliers show be very few or none for low resolution
structures.
On Thu, Apr 23, 2015 at 6:25 PM, Gert Bange
They have, it is call PDB_REDO. You can download the maps and refined structure
there.
http://www.cmbi.ru.nl/pdb_redo/
Dan
Its not just the Ramachandran outliers - the attached metrics summary
courtesy of the PDB raises a lot of questions about the accuracy of
this structure
As for Nature being right, it was an attempt at humor.
Dear crystallographers,
The PDB entry
@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] on behalf of Mark J
van Raaij [mjvanra...@cnb.csic.esmailto:mjvanra...@cnb.csic.es]
Sent: Thursday, April 23, 2015 11:49 AM
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!
How reliable is too general
.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Mark J van Raaij
[mjvanra...@cnb.csic.es]
Sent: Thursday, April 23, 2015 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!
How reliable is too general a question - it depends
] on behalf of Misbah ud Din
Ahmad [misba.ah...@gmail.com]
Sent: Thursday, April 23, 2015 11:03 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!
Dear crystallographers,
The PDB entry
http://www.rcsb.org/pdb/explore.do?structureId=3BDN
has 16.5% Ramachandran
On Thursday, 23 April, 2015 18:25:35 Gert Bange wrote:
Dear Mishba,
Just check density vs model by simply open 'Coot',
Go to: 'File' - 'Fetch PDB Map using EDS'
Type the pdb entry into the field - enjoy the densities.
If you want to pursue the plausibility of specific outliers
you
.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Mark J van
Raaij [mjvanra...@cnb.csic.es]
Sent: Thursday, April 23, 2015 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!
How reliable is too general a question
, 2015 1:05 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!
The abstract of the papers says they used MIR.
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http
: Thursday, April 23, 2015 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!
How reliable is too general a question - it depends on what you want to
know.
At 3.9Å they could probably place the phosphate atoms quite well and
see the general
Isn't the only criteria for EDS that calculated R (by EDS) is +/- 5% of
reported R?
On Thu, Apr 23, 2015 at 12:35 PM, Misbah ud Din Ahmad misba.ah...@gmail.com
wrote:
Dear Gert,
I just did that and I wonder how these structures end there !!!
@ Sabine: I was talking about Ramachandran
] On Behalf Of Phoebe A.
Rice
Sent: Thursday, April 23, 2015 12:46 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!
Dear Misbha,
Before you throw stones at other peoples' work:
- have YOU tried to refine a structure at 3.9A, particularly with older
.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Mark J van
Raaij [mjvanra...@cnb.csic.es]
Sent: Thursday, April 23, 2015 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!
How reliable is too general a question
At around 4.0 A resolution one normally cannot talk about accuracy. The
density will at most locations not warrant any detailed interpretation.
If, at 4.0 A resolution, you move atoms around a bit, you will not see
significant changes in R/Rfree. So, you can do whatever you want, more
or less.
Hi,
I entirely agree with Phoebe. This is 2008 structure (publish date, so
refinement was probably done in 2007) - that is before all the new methods
and tools for low-res refinement became available.
Now, let's have a closer look... Given rather large amount of various
geometry outliers (in
I feel rather uncomfortable and cornered with the aggressive replies and
phrases like throwing stones, public humiliation etc., which suggest
that I have some personal enmity with the author. The structure is in the
public domain and questions can be asked about it. I as a beginner in
: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!
I feel rather uncomfortable and cornered with the aggressive replies and
phrases like throwing stones, public humiliation etc., which suggest that I
have some personal enmity with the author. The structure is in the public
domain and questions
How reliable is too general a question - it depends on what you want to know.
At 3.9Å they could probably place the phosphate atoms quite well and see the
general fold of the protein.
Finer details will be less reliable, i.e. where the exact side-chains are etc.
They could probably have forced
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