Hi Firdous, You can use the CCP4 program sortwater to rename waters by chain. https://www.ccp4.ac.uk/html/sortwater.html The wwPDB sorts waters to the nearest chain as well (there was a time in the past where they put waters and ligands in a separate chain from the protein). They use the RCSB package MAXIT in the deposition pipeline. https://sw-tools.rcsb.org/apps/MAXIT/index.html <https://sw-tools.rcsb.org/apps/MAXIT/index.html> Regards. Mitch
On Wed, Aug 13, 2025 at 7:37 AM Kelvin Lau < [email protected]> wrote: > It is definitely possible, however, after PDB deposition all the waters > will be sorted out into chain S anyways… same with ligands, and sugars. > > > > -- > Kelvin Lau > > https://people.epfl.ch/kelvin.lau > > > Scientist - Protein production and structure core facility – PTPSP > > Co-President – EPFL Scientific Staff Association – ELSA > > > EPFL SV PTECH PTPSP > AI 2146 (Bâtiment AI) > Station 19 > CH-1015 Lausanne > Switzerland > Email: [email protected] <[email protected]> > Phone: +41 21 69 30267 <+41%2021%2069%C2%A030267> > > If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267> > > > > > > On 13.08.2025, 13:21, "CCP4 bulletin board on behalf of Firdous Tarique" < > [email protected] on behalf of [email protected]> wrote: > > > > 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://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## 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/
