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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 En/na Dirk Kostrewa ha escrit: > > Does the PDB really renumber waters and ions before deposition? If yes, > than any reference in the paper to specific waters and ions might be > difficult/impossible to find in the deposited structure ... Usually, the > paper is written prior to deposition. > > Dirk. > Well, in fact if I had to suggest a convention, I would say: first deposit the structure(s) you're happy with, then do all your clever analyses and finally write the paper ;-) This way, no mismatches (other than typos?) between the final coordinates file and the published paper. I don't agree with all PDB conventions, but I agree with Eleanor in that their work is essential to keep things tidy, whatever version of "tidiness" they choose. Cheers, Miguel > Eleanor Dodson wrote: >> I dont like being told what to deposit, but on the other hand I am >> very very grateful when I download a structure if the depositors have >> been forced to follow a defined convention. (Note the recent >> correspondence about Malenate) >> >> It is up to us if we think the conventions are restrictive to make a >> case for change - but please dont disregard them - we hope the >> structures we deposit have some scientific interest to others, and the >> users deserve consideration - I guess they represent the tax payers.. >> >> Eleanor >> >> Gerard DVD Kleywegt wrote: >> >>>> the guys at EBI always renumber the solvent molecules, ions and/or >>>> ligands following a so-called uniformatory convention during >>>> coordinate deposition. >>> >>> >>> i'm sure kim will respond and explain how this is done for a good reason >>> >>>> Would it be possible to make a lobby and get the PDB NOT TO CHANGE >>>> anything we don?t want to have changed in the structures that are >>>> supposed to be >>> >>> >>> alternatively - we could all follow the convention from the start >>> >>>> This is as if I went to the bank to deposit some money in what's >>>> theore- tically my account and that it was actually the clerk that >>>> told me how much I have to deposit ! >>> >>> >>> since you need to deposit in order to publish (not to mention the >>> fact that most structures are paid for by tax-payers' money) i would >>> argue that the simile is wrong. it is more like going to the *tax >>> office*. and, yes, the tax man does tend to tell you how much you >>> have to deposit ... [of course, if you live in Natureland, >>> Scienceland or Cellland, you may get away with tax evasion ...] >>> >>> --dvd >>> >>> ****************************************************************** >>> Gerard J. Kleywegt >>> [Research Fellow of the Royal Swedish Academy of Sciences] >>> Dept. of Cell & Molecular Biology University of Uppsala >>> Biomedical Centre Box 596 >>> SE-751 24 Uppsala SWEDEN >>> >>> http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] >>> ****************************************************************** >>> The opinions in this message are fictional. Any similarity >>> to actual opinions, living or dead, is purely coincidental. >>> ***************************************************************** >>> * >> >> > > - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: [EMAIL PROTECTED] - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFFdyzLF6oOrDvhbQIRAtEOAJsFVyuvT3yc/DdqePMy6mYBuHrS2ACfZK+b OtM8h+zkW5NdG9Yj/Un9ZSs= =Dw2e -----END PGP SIGNATURE-----
