Re: [ccp4bb] PDB structure validation

2013-10-31 Thread Debasish Chattopadhyay
: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB structure validation Try JCSG QC server: http://smb.slac.stanford.edu/jcsg/QC/ All our structures go through this server before submitted to the PDB and we rarely get any issues back from PDB. Thanks, Abhinav

Re: [ccp4bb] PDB structure validation

2013-10-31 Thread Kumar, Abhinav
AM To: Debasish Chattopadhyay Cc: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] PDB structure validation Yes, the intention at the PDB sites is to make available a standalone validation server that will run exactly the same validation tests that have been in

Re: [ccp4bb] PDB structure validation

2013-10-31 Thread Aaron Thompson
.nesg.org/ > > Rongjin Guan > > *From:* Bosch, Juergen > *Date:* 2013-10-31 11:48 > *To:* CCP4BB > *Subject:* Re: [ccp4bb] PDB structure validation > You do use Coot and look at the density plots right ? > Phenix will essentially do the same but in text form (unless

Re: [ccp4bb] PDB structure validation

2013-10-31 Thread rjguan
we have a PSVS server, and welcome people to try and give back comments: http://psvs-1_5-dev.nesg.org/ Rongjin Guan From: Bosch, Juergen Date: 2013-10-31 11:48 To: CCP4BB Subject: Re: [ccp4bb] PDB structure validation You do use Coot and look at the density plots right ? Phenix will essentially

Re: [ccp4bb] PDB structure validation

2013-10-31 Thread Raji Edayathumangalam
dhyay > *Cc:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] PDB structure validation > > ** ** > > Yes, the intention at the PDB sites is to make available a standalone > validation server that will run exactly the same validation tests that have > been introduced for

Re: [ccp4bb] PDB structure validation

2013-10-31 Thread Debasish Chattopadhyay
Thanks Randy. That would be fantastic. From: Randy Read [mailto:rj...@cam.ac.uk] Sent: Thursday, October 31, 2013 11:02 AM To: Debasish Chattopadhyay Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB structure validation Yes, the intention at the PDB sites is to make available a standalone

Re: [ccp4bb] PDB structure validation

2013-10-31 Thread Randy Read
Yes, the intention at the PDB sites is to make available a standalone validation server that will run exactly the same validation tests that have been introduced for recent depositions. My understanding is that this server is currently being tested and will be rolled out to the community someti

Re: [ccp4bb] PDB structure validation

2013-10-31 Thread Debasish Chattopadhyay
for all the suggestions. Debasish From: Bosch, Juergen [mailto:jubo...@jhsph.edu] Sent: Thursday, October 31, 2013 10:48 AM To: Debasish Chattopadhyay Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB structure validation You do use Coot and look at the density plots right ? Phenix will

Re: [ccp4bb] PDB structure validation

2013-10-31 Thread Sebastiano Pasqualato
From: longingforadmiss...@gmail.com [mailto:longingforadmiss...@gmail.com] On > Behalf Of Mahesh Lingaraju > Sent: Thursday, October 31, 2013 10:32 AM > To: Debasish Chattopadhyay > Subject: Re: [ccp4bb] PDB structure validation > > Hi > > One can do an unofficial validation i

Re: [ccp4bb] PDB structure validation

2013-10-31 Thread Bosch, Juergen
all. Debasish From: longingforadmiss...@gmail.com<mailto:longingforadmiss...@gmail.com> [mailto:longingforadmiss...@gmail.com] On Behalf Of Mahesh Lingaraju Sent: Thursday, October 31, 2013 10:32 AM To: Debasish Chattopadhyay Subject: Re: [ccp4bb] PDB structure validation Hi One can

Re: [ccp4bb] PDB structure validation

2013-10-31 Thread Debasish Chattopadhyay
: longingforadmiss...@gmail.com [mailto:longingforadmiss...@gmail.com] On Behalf Of Mahesh Lingaraju Sent: Thursday, October 31, 2013 10:32 AM To: Debasish Chattopadhyay Subject: Re: [ccp4bb] PDB structure validation Hi One can do an unofficial validation in Adit server ( one of the pdb deposition services

Re: [ccp4bb] PDB structure validation

2013-10-31 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Debasish Chattopadhyay, in my experience someone from the PDB always contacted me during the deposition process and discussed the necessary modifications which included (and possibly exceeded) the issues raised by the validation report, i.e. the

Re: [ccp4bb] PDB structure validation

2013-10-31 Thread Debasish Chattopadhyay
Molprobity doesn't analyze density fit. New PDB validation now reports density fit analysis etc. From: Bosch, Juergen [mailto:jubo...@jhsph.edu] Sent: Thursday, October 31, 2013 10:28 AM To: Debasish Chattopadhyay Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB structure validation

Re: [ccp4bb] PDB structure validation

2013-10-31 Thread Bosch, Juergen
yes, indeed. visit this site and make sure you get all green lights http://molprobity.biochem.duke.edu Jürgen On Oct 31, 2013, at 11:25 AM, Debasish Chattopadhyay wrote: I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go ba

[ccp4bb] PDB structure validation

2013-10-31 Thread Debasish Chattopadhyay
I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish Chattopa