Hi Elise, Not exactly what you are asking for, but lsqman will compare waters between structures with a cut-off. (However, it will not renumber the waters as you wanted) http://xray.bmc.uu.se/usf/lsqman_man.html#S71
If you want to look at waters related by NCS in a single PDB file with multiple macromolecule chains, then you can use sortwater which will renumber NCS related waters with the same residue number but different chain identifiers. (I think watncs also does a similar thing, but I have not used it). Regards, Mitch -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dom Bellini Sent: Tuesday, October 29, 2013 3:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs Hi Elise, How about taking the homologue structure with highest number of waters and use it to run molecular replacement on all other datasets? Then you could keep only the good waters (manually unfortunately) which will ensure they will all have the same numbers. Probably not the fastest way but it should give what I think you were asking for? HTWorks D ________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Swastik Phulera [swastik.phul...@gmail.com] Sent: 29 October 2013 21:16 To: ccp4bb Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs Downloading structures of the same homologous family with blast. Then superimpose them on a reference structure. You may then try to look at over lapping water molecules On 30 Oct 2013 02:23, "Elise B" <ek...@case.edu<mailto:ek...@case.edu>> wrote: Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that exist in roughly the same position in each PDB share the same residue number. Basically, I want to compare solvent molecule coordinates and assign similar locations the same name in each structure. What would be the best strategy for re-numbering the water molecules such that those with similar coordinates in all the structures receive the same residue number? I'd appreciate any suggestions. Elise Blankenship -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
