Hi Yes. I have it mixed in my head as my water chains are renamed to the way Firdous is desiring.
My waters are typically named as chain S in Coot. Upon deposition, the PDB renames them accordingly and sticks them back to the polypeptide chain that is closer (https://www.wwpdb.org/documentation/procedure#toc_6). -- 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]<mailto:[email protected]> Phone: +41 21 69 30267<tel:+41%2021%2069%C2%A030267> If unreachable: +41 21 69 34494<tel:+41%2021%2069%C2%A030267> On 13.08.2025, 15:15, "Oganesyan, Vaheh" <[email protected]<mailto:[email protected]>> wrote: I think this statement is incorrect. PDB deposition does exactly what you want to do, Firdous: the software will sort the waters you have in file and apply chain Id based of protein chain proximity. Vaheh Oganesyan, Ph.D. [cid:[email protected]] R&D | Biologics Engineering One Medimmune Way, Gaithersburg, MD 20878 T: 301-398-5851 [email protected]<mailto:[email protected]> From: CCP4 bulletin board <[email protected]> On Behalf Of Kelvin Lau Sent: Wednesday, August 13, 2025 8:37 AM To: [email protected] Subject: Re: [ccp4bb] rearrangement of water molecules with correct Chain id 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]<mailto:[email protected]> Phone: +41 21 69 30267<tel:+41%2021%2069%C2%A030267> If unreachable: +41 21 69 34494<tel:+41%2021%2069%C2%A030267> On 13.08.2025, 13:21, "CCP4 bulletin board on behalf of Firdous Tarique" <[email protected]<mailto:[email protected]> on behalf of [email protected]<mailto:[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 ________________________________ Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. ######################################################################## 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/
