Re: [ccp4bb] identifying bound ions
Dear Herman, the "water scrutinizer" option of XPAND does this -. http://www.msg.ucsf.edu/local/programs/ono/manuals/xpand_man.html#S7 best wishes, Kay On Tue, 31 Jul 2018 12:39:01 +, herman.schreu...@sanofi.com wrote: >Dear BB, > >I know it has been discussed some time ago, but a google search did not come >up with anything useful. > >I need a program which analyzes the bound waters and suggests whether a >particular water might be a chloride, calcium, sulfate, sodium or something >else. Preferably a program that can be run off-line (not a web server), but if >there is no choice, we will use a webserver as well. > >Thank you for your suggestions! >Herman > > > > > > >To unsubscribe from the CCP4BB list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] identifying bound ions
There is an option in phenix.refine to do this, described here: Automated identification of elemental ions in macromolecular crystal structures. Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ, Richardson JS, Terwilliger TC, Adams PD Acta Cryst. D70, 1104-1114 (2014). Pavel On Tue, Jul 31, 2018 at 5:39 AM, wrote: > Dear BB, > > > > I know it has been discussed some time ago, but a google search did not > come up with anything useful. > > > > I need a program which analyzes the bound waters and suggests whether a > particular water might be a chloride, calcium, sulfate, sodium or something > else. Preferably a program that can be run off-line (not a web server), but > if there is no choice, we will use a webserver as well. > > > > Thank you for your suggestions! > > Herman > > > > > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] identifying bound ions
Dear Herman, You can try this out, a web server though: https://csgid.org/metal_sites Cheers, Arnaud From: CCP4 bulletin board on behalf of "herman.schreu...@sanofi.com" Reply-To: "herman.schreu...@sanofi.com" Date: Tuesday 31 July 2018 at 14:39 To: "CCP4BB@JISCMAIL.AC.UK" Subject: [ccp4bb] identifying bound ions Dear BB, I know it has been discussed some time ago, but a google search did not come up with anything useful. I need a program which analyzes the bound waters and suggests whether a particular water might be a chloride, calcium, sulfate, sodium or something else. Preferably a program that can be run off-line (not a web server), but if there is no choice, we will use a webserver as well. Thank you for your suggestions! Herman To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] identifying bound ions
Hi Herman, Whatcheck does his as well for the metals. Chloride is not highly coordinated, likes nitrogens, and has long coordination lengths (over 3A). Sulfate gives huge blobs and sticks out in difference density or ridiculously low B-factors. HTH, Robbie Sent from my Windows 10 device From: CCP4 bulletin board on behalf of Christian Roth Sent: Tuesday, July 31, 2018 2:47:25 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] identifying bound ions Hi Herman, out of the top of my head I think there is an option in Coot to check if the water is highly coordinated and might be an ion and I think there was also a function in Phenix to check for ions. Cheers Christian mailto:herman.schreu...@sanofi.com>> schrieb am Di., 31. Juli 2018, 14:39: Dear BB, I know it has been discussed some time ago, but a google search did not come up with anything useful. I need a program which analyzes the bound waters and suggests whether a particular water might be a chloride, calcium, sulfate, sodium or something else. Preferably a program that can be run off-line (not a web server), but if there is no choice, we will use a webserver as well. Thank you for your suggestions! Herman To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] identifying bound ions
Hi Herman, out of the top of my head I think there is an option in Coot to check if the water is highly coordinated and might be an ion and I think there was also a function in Phenix to check for ions. Cheers Christian schrieb am Di., 31. Juli 2018, 14:39: > Dear BB, > > > > I know it has been discussed some time ago, but a google search did not > come up with anything useful. > > > > I need a program which analyzes the bound waters and suggests whether a > particular water might be a chloride, calcium, sulfate, sodium or something > else. Preferably a program that can be run off-line (not a web server), but > if there is no choice, we will use a webserver as well. > > > > Thank you for your suggestions! > > Herman > > > > > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
