The server seems to be up again. Give it another try.
Cheers,
Robbie
Date: Tue, 2 Aug 2011 12:43:43 -0700
From: bourn...@yahoo.com
Subject: Re: [ccp4bb] Sodium ion vs. Water
To: robbie_joos...@hotmail.com; CCP4BB@JISCMAIL.AC.UK
Hi Robbie and all
Dear CCP4 experts,
I would like to ask if there is a clear way to distinguish Na+ and HOH
molecules in the electron density map. The table I have suggests Na
to O distance lies between 2.35 and 2.45 that is very hard to discern
the difference of these two candidates. Na+ may have several
I asked the CCP4 experts this question a while back--maybe try
searching the archive? There were some very helpful comments.
Jacob
On Tue, Aug 2, 2011 at 1:24 PM, Young-Jin Cho yj...@brandeis.edu wrote:
Dear CCP4 experts,
I would like to ask if there is a clear way to distinguish Na+ and HOH
: [ccp4bb] Sodium ion vs. Water
To: CCP4BB@JISCMAIL.AC.UK
Dear CCP4 experts,
I would like to ask if there is a clear way to distinguish Na+ and HOH
molecules in the electron density map. The table I have suggests Na
to O distance lies between 2.35 and 2.45 that is very hard to discern
, August 2, 2011 2:20 PM
Subject: Re: [ccp4bb] Sodium ion vs. Water
Dear Young-Jin,
If you model it as water, you can use WASP. It's an old program but still
accesible here: http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl
Cheers,
Robbie
Date: Tue, 2
Hi Christina,
The WASP server seems to working at this location (about half way down the
page):
http://www.jcsg.org/prod/scripts/validation/sv2.cgi
I hope that helps.
Take Care,
Sean
P212121
http://store.p212121.com/
Hi,
I decided to give the server a try...and the output is:
FILE NOT FOUND:
/prod/tmp/individual_validation/output_wasp/25854/bindividual6Na.ion
Either my pdb does not have any metal ions or this server is currently not
working.
Sujata
On Tue, Aug 2, 2011 at 5:04 PM, Sean Seaver
Hi Jacob,
Darn that site doesn't seem to be working. I generated the files ion files and
thought it was good to go, but didn't view the outputs.
Apologies,
Sean Seaver
P212121
http://store.p212121.com/
Search for Metal Cordination sites in Proteins.
It takes you to a site set up by Marjorie Harding which gives a table of
known metal coordination extracted from the PDB including Na.
Of course there may be errors in the PDB entries but it is very helpful I
find
Eleanorr
On Tue, 2 Aug 2011
