Dear Mark, It also appears to me that the formatting of the cif matters. In my case for some reason, I can't get Coot 0.5/0.6 to read the cif file written by Refmac/Sketcher of CCP4i 6.1.1.
I've compared the cif file from PRODRG and CCP4i for the same monomer, and found that that the column positions for certain entries are different. I've edited CCP4i's cif file to match the column positions of PRODRG's cif file, and I can get Coot to read it properly and let me do real space refinement. Still, I feel that there may be some other things that I've overlooked because this is quite unexpected... Regards, Peter > Date: Mon, 31 Aug 2009 01:17:39 +0200 > From: [email protected] > To: [email protected] > CC: [email protected] > Subject: Re: [ccp4bb] Problem with Coot reading monomer library file. > > Peter, Paul, > a couple of months ago I had a similar problem - older versions of, in > this case, Refmac, working with a cif file and a new version not. > It turned out newer Refmacs are more picky about the types of > "returns" at the end of each line in the file. > I had been editing the file with MacOSX textedit and somehow the > resulting file contained the wrong kind of "returns" ("hard" or > "soft", I can't remember exactly), and not all info from the cif file > was actually read into Refmac. > It took me several days and help of Garib Murshudov, the main Refmac > author, to figure this out so, Peter, only just over 10 hours was not > bad! > Paul, apologies for the above description, probable a > programming/computer expert like you would have formulated it a lot > better... > Peter, could it be that your Coot 0.1 is somehow also coupled to an > older, more tolerant, Refmac (perhaps you did this test on another > computer?) and your Coot 0.6 uses a newer Refmac version? > Mark > > > Quoting Peter Chan <[email protected]>: > > > > > Dear Eric, > > > > Thank you very much for your suggestion. It worked. > > > > Dear Paul, > > > > Thank you for your kind offer with the help (and for writing such a > > wonderful program + providing users with support!). I will compare > > the cif files and see if I can pick out the differences... > > > > Sincerely, > > Peter > > > > > > > > Hi Peter, > > Did you try making a cif using the Dundee Prodrg server? > > http://davapc1.bioch.dundee.ac.uk/prodrg/ > > Eric > > -- Eric Ortlund, Ph.D.Assistant ProfessorDepartment of > > BiochemistryEmory University School of Medicine1510 Clifton Road, > > NE, Room G235Atlanta, GA 30322Tel 404-727-5014 Fax > > [email protected] > > > > > >> Date: Sat, 29 Aug 2009 07:02:12 +0100 > >> From: [email protected] > >> To: [email protected] > >> Subject: Re: [ccp4bb] Problem with Coot reading monomer library file. > >> > >> Peter Chan wrote: > >> > Dear Crystallographers, > >> > > >> > I've been spending >10 hours trying (googling, manually editting cif > >> > files based on templates in Coot's library, asking around, rtfm and > >> > reading this bbs) to figure out why Coot the geometric restraints > >> > wouldn't load. > >> > >> I can think of no reason why 0.1 would work and 0.6 would not. If you > >> want me to investigate, please send the PDB and cif dictionary. > >> > >> Regards, > >> > >> Paul. > >> > > > > _________________________________________________________________ > > Stay in the loop and chat with friends, right from your inbox! > > http://go.microsoft.com/?linkid=9671354 > > _________________________________________________________________ New! Get to Messenger faster: Sign-in here now! http://go.microsoft.com/?linkid=9677407
