Re: [ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

2018-03-13 Thread Paul Emsley
On 13/03/2018 07:36, M T wrote: So finally the solution was easy access... Thanks to someone who suggest me to do that, I created a new user, to verify if coot was ok under that session, and it was fine. Then I went back on my session, I removed the files below: 0-coot-history.py

Re: [ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

2018-03-13 Thread M T
So finally the solution was easy access... Thanks to someone who suggest me to do that, I created a new user, to verify if coot was ok under that session, and it was fine. Then I went back on my session, I removed the files below: 0-coot-history.py 0-coot-history.scm 0-coot.state.py

Re: [ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

2018-03-12 Thread Paul Emsley
On 12/03/18 14:05, M T wrote: > Dear all, > > I restart this topic because the problem was finally not solved... You give me an opportunity to comment, I had previously missed the boat while traveling. > > Summary: > - I am working on a structure with an unnatural ligand and I want to > refine

Re: [ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

2018-03-12 Thread M T
Dear all, I restart this topic because the problem was finally not solved... Summary: - I am working on a structure with an unnatural ligand and I want to refine this ligand using coot. - Each time I try to import the .cif of my ligand produced by PRODRG web server or through CCP4/ProDrg, coot

Re: [ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

2018-03-06 Thread M T
Last update... Everything works well with the same files and the same Coot version on an other computer. The problem may come from the os of my computer which is too old and has to be upgraded. Thank you for your help. 2018-03-06 9:20 GMT+01:00 M T : > Dear all, > > I did

Re: [ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

2018-03-06 Thread M T
Dear all, I did something very simple... Starting from the pdb I obtained from PRODRG server (manual drawing, then transfer to PRODRG and download of the pdb from server), in CCP4 I used ProDrg to generate a new .cif and a new .pdb. After I used "View Job Results (ew style)" to open my new pdb

Re: [ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

2018-03-05 Thread Eleanor Dodson
Herman is right - as long as refmac reads your generated DRG that is the dictionary it will use.. My way of doing this sort of thing: Start with COOT with the DRG coordinates and ProDRG dictionary and try a bit of real space refinement. Coot should move the coodinates a bit and you should see