Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

, 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

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

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 uncomfortable and cornered with the aggressive replies and > phrases like &q

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

to > me. > > -- > *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 O

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

r anyone else finds > problems 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

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

i/10.1107/S0907444913029168/abstract), > > > > > but the referees could have been a bit more critical. They should have > > at least seen that the supplemental table 1 did not show any > > Ramachandran statistics. We can only speculate what happened. I'm > > guessing that the authors didn't finis

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

lletin 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 r

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

t: Re: [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 op

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

data. 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,

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

general glory of a Nature paper. 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

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

: [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 th

Re: [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 can be asked about it. I as a beginner in crystallo

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

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 mode

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

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.

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

>> From: CCP4 bulletin board >> [CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] on behalf of Mark J >> van Raaij [mjvanra...@cnb.csic.es<mailto:mjvanra...@cnb.csic.es>] >> Sent: Thursday, April 23, 2015 11:49 AM >> To: CCP4BB@JISCMAIL.AC.UK<mail

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

They have, it is call PDB_REDO. You can download the maps and refined structure there. http://www.cmbi.ru.nl/pdb_redo/ Dan

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

t;> > >> 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

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

Sent: Thursday, April 23, 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, Spa

[ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

we have >> better tools for this these days. >> >> >> >> 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: CCP4

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

r this these days. > > > > 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 Outlier

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

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

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

days. 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 depen

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] 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 st

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 fold of the protein. Finer details will be less reliable, i.e. where the exact side-chains are etc. They could probably have forced mor

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

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

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

lletin board [CCP4BB@JISCMAIL.AC.UK] 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 ha

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

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 wrote: > Dear Gert, > I just did that and I wonder how these structures end there !!! > > @ Sabine: I was talking about Ramachandran outliers. I had learnt th

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

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 < gert.ba...@sy

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

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

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

It was published in Nature so it must be right :) ... 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 Ramacha

[ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

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%