Be aware that WASP does not take into account symmetry-related atoms when analysing the co-ordination sphere of a potential ion; this becomes clear when you look at the source code (http://biochem.wustl.edu/~enrico/wasp.htm) & see that it only reads the ATOM & HETATM records from the PDB file, and it never asks you for cell & space group info (see http://biochem.wustl.edu/~enrico/README.htm - scroll down to the end). In my view this is a serious deficiency considering that most ions (at least the ones that are likely to be confused with water molecules) reside on the surface of a protein where at least some of the contacts are likely to be to symmetry-related atoms.
Caveat emptor! -- Ian > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Jacob Keller > Sent: 21 August 2007 16:55 > To: [email protected] > Subject: Re: [ccp4bb] Wasp web server > > There is a nice web server which does wasp et al: > > http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl > JPK > > > ==============Original message text=============== > On Tue, 21 Aug 2007 10:48:00 am CDT Marko Hyvonen wrote: > > > > > Are there any methods that allow one to input such ions as possible > > candidates? What would be ideal is to have a program that > says something > > like "The density peak at x,y,z, has a .0973 chance of > being real. It is > > only 2.2 Å from N7 of G12, precluding water. Based on the > mother liquor > > ingredient list you provided, there is a 0.75 chance that > this is Mg++, > > 0.25 chance it is Na+ (or whatever), based on a > > crystallographically-derived library of 40,000 structural > variants of the > > ribosome. > > Not quite what you ask for, but WASP does something along > those lines. > > From the output of the program: > > ############################################################## > ########### > ############################################################## > ########### > > > WASP --- WAter Screening Program > > > > Version 1.0 1995 > > > > Copyright (c) Murad Nayal & Enrico Di Cera > 1995 > > > > > This program will take a Protein Data Bank structural file > with solvent > electron density peaks designated as water oxygens. Based > on simple > structural criteria it will pick out the peaks that could > be metal ions > (Na+, Li+, Mg+2, Ca+2). The chosen peaks are subsequently > written to 4 > pdb-formatted files one for each ion. The temperature > factor field is > replaced by the calculated ion-specific valence of that > solvent peak. > > > Reference: Nayal, M., & Di Cera, E. (1996) J. Mol. Biol. > 256: 228-234 > > > ############################################################## > ########### > ############################################################## > ########### > > See http://biochem.wustl.edu/~enrico/ > > Marko > > > > > > Bill > > > > > _____________________________________ > > Marko Hyvönen > Department of Biochemistry > University of Cambridge > http://www-cryst.bioc.cam.ac.uk/~marko tel: +44-(0)1223-766 > 044 / 760 468, fax: 766 002 > _______________________________________ > ===========End of original message text=========== > > > > *********************************** > Jacob Keller > Northwestern University > 6541 N. Francisco #3 > Chicago IL 60645 > (847)467-4049 > [EMAIL PROTECTED] > *********************************** > > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
