Hi Patrick, while I agree with Tim this task may be a bit less straightforward than it appears, I think you can get ballpark numbers by looping over all PDB entries and searching for a keyword in PROGRAM card. All you need is to make an upfront definition of what you count as "phenix", "ccp4", "shelx", "main", "eref", "molly", "mopro", "refmac", "frog" (I have a full list somewhere). I do this every few months. Using CCTBX it is a less than half-page long script.
All in all, it is definitely possible, just may be not super-accurate! Pavel On Sat, Jan 24, 2015 at 2:44 PM, Patrick <patrick.coss...@inbox.com> wrote: > Hi Tim, > > Thank you for the clarification. > > Is there a way to extract from the PDB all the CCP4/Phenix structures then? > From your answer I take it there is no way? > > Patrick > > > -----Original Message----- > > From: t...@shelx.uni-ac.gwdg.de > > Sent: Sat, 24 Jan 2015 20:35:54 +0100 > > To: ccp4bb@jiscmail.ac.uk > > Subject: Re: [ccp4bb] extracting PHENIX structures > > > > Dear Patrick, > > > > those entries are entered by the user and not very reliable. E.g. I > > would not say 'CCP4 refined' but 'refmac5 refined' or 'restrain > > refined', as much as 'SHELXL refined' and 'phenix.refine refined'. This > > makes two different ways between the two of us - take all depositors and > > I guess that's one explanation for why to different search types produce > > two different results. > > > > Best, > > Tim > > > > On 01/24/2015 06:41 PM, Patrick wrote: > >> Hi, > >> > >> not directly related but I wanted to know how to extract from the PDB > >> all the PHENIX/CCP4 refined structures currently deposited. > >> > >> Do I use the "text" search in quarry to get the result or do I use the > >> software? > >> > >> I tried it for both but seems to give different results (no's). > >> > >> I tried for another refinement package (shelx) and same, different no's > >> > >> Using software, and looking for contains 320 > >> > >> using text search 130 > >> > >> Is there another way to get structure of a certain resolution ? > >> > >> Patrick > >> > >> ____________________________________________________________ > >> Can't remember your password? Do you need a strong and secure password? > >> Use Password manager! It stores your passwords & protects your account. > >> Check it out at http://mysecurelogon.com/password-manager > >> > > > > -- > > Dr Tim Gruene > > Institut fuer anorganische Chemie > > Tammannstr. 4 > > D-37077 Goettingen > > > > GPG Key ID = A46BEE1A > > ____________________________________________________________ > FREE ONLINE PHOTOSHARING - Share your photos online with your friends and > family! > Visit http://www.inbox.com/photosharing to find out more! >
