Re: [ccp4bb] Sulphate or phosphate?
Not very elegant way of doing what you want but as a last resort I used distance criteria. P-O distance is 1.6A, S-O distance is 1.4A. Provided your coordinate error is in the range of 0.1A you may cautiously suggest one or the other. However, it may be impossible to prove that what you see is not a mixture of both. Regards, Vaheh Oganesyan, PhD www.medimmune.com -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David Schuller Sent: Tuesday, July 31, 2018 9:39 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Sulphate or phosphate? How can one distinguish between a sulphate or phosphate in an electron density map? Both are present in the mother liquor, and resolution is in the range of 1.75 - 2.25 A -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu To unsubscribe from the CCP4BB list, click the following link: https://clicktime.symantec.com/a/1/Nqayc8hNA0CibV9rgPxsew5F9lJ-EFZMtnajSeJqGcA=?d=b3aSQTOaO64IQYsIn3CPYoKfOtDU4_-vH5Rx0GJU-o2i1olOuKzm571t92z342L8Vpe77PS6t68Hj6Erw8iU1gbK0zZfvQxt-2WsDy8HrYF-F23OaYvTj0tK3QKs9smFywd5DnI_EVqqoa0eE5Si6HBDs-Z-_T_2TTlIj2IT_1wim9OaZGf_f0mzGwgp2u98gM14ADWl8LeFmpBz8YS_gv56eMGDZJ_3JeAKra_jTexwqzrVVSDtDe4HlOhZ0ZG8-BAhAJQerHpMBuSWwY9B96V-NVkbnYo6Yl8LRN2yMdboNhGLA2-6i2rI-RU4pmsjgNp-VmO_UwlHliLTmwaXWCFThjBc3MS6TsMq1fgHk3O5r6DgPZDFlvBUbRCyHJ0y&u=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1 To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] Sulphate or phosphate?
If the site is not really selective, I would model the one with the highest concentration. If your data are really good an anomalous. Map would help. Cheers, Robbie Sent from my Windows 10 device From: CCP4 bulletin board on behalf of David Schuller Sent: Tuesday, July 31, 2018 3:38:38 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Sulphate or phosphate? How can one distinguish between a sulphate or phosphate in an electron density map? Both are present in the mother liquor, and resolution is in the range of 1.75 - 2.25 A -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] Sulphate or phosphate?
You might be able to distinguish sulfate from phosphate by examining hydrogen bonding partners. Phosphate can donate one or two hydrogen bonds at neutral pH values, whereas sulfate is usually only a hydrogen bond acceptor. (Having said that, we have published a structure where a sulfate clearly interacts with a glutamate, the later of which which may or may not be protonated at near neutral pH.) ___ Roger S. Rowlett Gordon & Dorothy Kline Professor, Emeritus Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-723-7245 email: rrowl...@colgate.edu On Tue, Jul 31, 2018 at 9:38 AM, David Schuller wrote: > How can one distinguish between a sulphate or phosphate in an electron > density map? Both are present in the mother liquor, and resolution is in > the range of 1.75 - 2.25 A > > > -- > === > All Things Serve the Beam > === >David J. Schuller >modern man in a post-modern world >MacCHESS, Cornell University >schul...@cornell.edu > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=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&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=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&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] Sulphate or phosphate?
How can one distinguish between a sulphate or phosphate in an electron density map? Both are present in the mother liquor, and resolution is in the range of 1.75 - 2.25 A -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=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&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=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&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[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&A=1
[ccp4bb] Postdoc Position at University of Goettingen
TheDepartment for Molecular Structural Biology at theGeorg-August-University Goettingen (http://www.uni-goettingen.de/msb)seeks to recruit a postdoctoral scientist in structural biology witha research focus directed towards the structure and dynamics ofprotein-RNA complexes. Theadvertised position is suitable for candidates with strong expertisein the preparation of protein-RNA complexes as well as X-ray crystallography and/or single particle cryo-EM. Aninitial contract of 2 years will be offered to the successfulcandidate. TheUniversity of Göttingen is committed to increase the number ofindividuals with disabilities in its workforce and thereforeencourages applications from such qualified individuals. Furthermore,the University of Göttingen seeks to increase the number of women inthose areas where they are underrepresented and therefore explicitlyencourages women to apply. The University of Göttingen is afamily-friendly employer and promotes the compatibility of family andcareer. Pleasesend your application as single PDF file by E-mail to Prof. Dr. RalfFicner (rfic...@uni-goettingen.de), Department of MolecularStructural Biology, GZMB, University Goettingen, Germany. Closingdate for applications: August 15, 2018. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] Postdoc position in Heidelberg, Germany
发自我的 iPad > 在 2018年7月19日，15:33，Grant 写道： > > Help develop antivirals against human norovirus using techniques such as > X-ray crystallography, cryo-EM, molecular biology, and cell culture. > Experience in structural biology, especially X-ray crystallography required. > Our lab is fully equipped to carryout most experiments in the drug > development. You will have opportunities to travel to international > collaborators, including Australia, Japan, and the USA. We have a great > working environment and plenty of freedom to explore your own projects and > ideas. > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] Second coordination sphere of a metal ion
Dear All, I am trying to connect to these two servers, but it seems like not working. http://tanna.bch.ed.ac.uk/index.html http://eduliss.bch.ed.ac.uk/MESPEUS/ Any alternate server that provides the same information? Thank you. Jobi To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
