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Thanks Nadir for your comment. I know about the "save to disk" option, but you only get it when you have selected a single PDB file.. As for the rest of my summary, here goes: Paul Emsley and Dima Klenchin pointed to the OCA mirror ar the Weizman institute (http://bioportal.weizmann.ac.il/oca-docs/mirrors.html) Cathy Lawson prefers the RCSB search tool. I did not use it before, I tried it after upgrading my Java RE to 1.5.9, and it works nicely in downloading multiple files, going to use this in the future. Ian Tickle points out that with OCA you cannot filter out structures without SFs deposited. I agree totally that this is necessary, Like Ian I always recalculate ED maps (or even re-refine sometimes!) before interpreting a model, especially if a ligand is modelled in. I only skip this when I just want to do MR... Flip -----Original Message----- From: Nadir T. Mrabet [mailto:[EMAIL PROTECTED] Sent: Tuesday, 17 October, 2006 11:28 To: Flip Hoedemaeker Cc: [email protected] Subject: Re: [ccp4bb]: OCA down Hi Flip: OCA is back to work, now. To my opinion, it is definitely the best tool around to search for/on structures. I, however, never managed to have these enclosed links work: STING, GRASS and Ramachandran. In OCA, you have to options to download coordinates: If you click on "complete with coordinates" the whole file is displayed in your browser window. If you then save it, it would include HTML strings. However, if, instead, you click on "Save to disk", then you directly download a clean pdb file you can directly use. Hope this helps. Nadir Mrabet Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM U-724 UHP - Nancy 1, School of Medicine Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: [EMAIL PROTECTED] Flip Hoedemaeker wrote: > Hi All, > > The OCA site of EBI seems to be down, which is unfortunate, since it > is my favorite PDB search tool at this moment. Perhaps time to do a > little survey on who likes which site to look for structures. What I > really like to be able to is to download a subsite of structures of > e.g. one particular protein without having to edit the downloaded > coordinates , for instance to remove HTML strings etc. > > Any suggestions? I'll post a summary! > > Flip > > -----<>--------------------- > Flip Hoedemaeker - Ph.D. CEO > Key Drug Prototyping BV > Kruislaan 406 > 1098 SM Amsterdam > The Netherlands > Tel +31-20-7512060 > Fax +31-20-2010115 > Mob +31-65-2451106 > Skype: fhoedem > www.keydp.com > -- > Important: This e-mail may contain legally privileged or confidential > information. If you are not the intended recipient it may be unlawful > for you to read, copy, distribute, disclose or otherwise use the > information contained in this e-mail. If you are not the intended > recipient of the e-mail, please delete the message and inform me of > the error. Errors and omissions may occur in the contents of this > e-mail arising out of or in connection with, for example, data > transmission, network malfunction or failure, machine or software > error. The contents of this e-mail are confidential. >
