Perhaps it's not common practice now, but water can assigned chain W. It's more convenient for down stream users of deposited structure, in my humble opinion, if molecules not covalently attached to a polymer chain are assigned a different chain ID.
Just a suggestion. Brent Brent Segelke, Ph.D. Bionanomaterials Group Leader Biosciences and Biotechnology Division Physical and Life Sciences Directorate Lawrence Livermore National Laboratory Office: (925) 424 4752 Work cell: (925) 918 3870 Email: [email protected] -----Original Message----- From: CCP4 bulletin board <[email protected]> On Behalf Of Phil Evans Sent: Wednesday, August 13, 2025 4:46 AM To: [email protected] Subject: Re: [ccp4bb] rearrangement of water molecules with correct Chain id There is a very old CCP4 program “sort water” which tries to do that, but I have no idea whether it still works :-( see https://urldefense.us/v3/__https://www.ccp4.ac.uk/html/sortwater.html__;!!G2kpM7uM-TzIFchu!zE8-k79IfTh_N7FTu31JbWRRdVFJ06CbDxGGrLcObMhXLJ4FmhGhrZHTNyq1ufRpgnuX5zoWd_m6pAcmfKoB2g$ Phil > On 13 Aug 2025, at 12:21, Firdous Tarique <[email protected]> wrote: > > CAUTION: This email originated from outside of the LMB: > [email protected]. > Do not click links or open attachments unless you recognize the sender and > know the content is safe. > If you think this is a phishing email, please forward it to > [email protected] > > -- > Hello everyone > > I have a situation where the water molecules in my protein chains are not > named correctly. For example I want water molecules in protein Chain A to be > named as Chain A but few water molecules are named as chain B. As the water > numbers in hundreds it is difficult to do it manually. Is there a way where > water molecules near chain A (let's say within 3.5 A) are automatically > renamed as chain A ? > > Any help is appreciated > > Best > > Firdous > > To unsubscribe from the CCP4BB list, click the following link: > https://urldefense.us/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!G2kpM7uM-TzIFchu!zE8-k79IfTh_N7FTu31JbWRRdVFJ06CbDxGGrLcObMhXLJ4FmhGhrZHTNyq1ufRpgnuX5zoWd_m6pAc3V7S8zA$ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://urldefense.us/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!G2kpM7uM-TzIFchu!zE8-k79IfTh_N7FTu31JbWRRdVFJ06CbDxGGrLcObMhXLJ4FmhGhrZHTNyq1ufRpgnuX5zoWd_m6pAc3V7S8zA$ This message was issued to members of https://urldefense.us/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!G2kpM7uM-TzIFchu!zE8-k79IfTh_N7FTu31JbWRRdVFJ06CbDxGGrLcObMhXLJ4FmhGhrZHTNyq1ufRpgnuX5zoWd_m6pAc6Eq-exg$ , a mailing list hosted by https://urldefense.us/v3/__http://www.jiscmail.ac.uk__;!!G2kpM7uM-TzIFchu!zE8-k79IfTh_N7FTu31JbWRRdVFJ06CbDxGGrLcObMhXLJ4FmhGhrZHTNyq1ufRpgnuX5zoWd_m6pAfqsdAerg$ , terms & conditions are available at https://urldefense.us/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!G2kpM7uM-TzIFchu!zE8-k79IfTh_N7FTu31JbWRRdVFJ06CbDxGGrLcObMhXLJ4FmhGhrZHTNyq1ufRpgnuX5zoWd_m6pAdndsnNNg$ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
