[ccp4bb] Ligand weak density in SHELXL
Dear all, I solved the structure of an enzyme at resolution of 1.1A with a bound substrate using Refmac5 and Coot for refinement/building. I have a very nice density for my ligand and a very good structure, as judged by Molprobity analysis. Now I'm using SHELXL to finish refinement but most of the density for my ligand disappears when I put it in, and it gets very high B factors. I though it could be some problem with the occupancy so I did a set of runs with different occupancies ranging from 0.2 to 1 and I got the best R factors when using 0.4/0.5 for the occupancy. However, I still have most of the ligand outside electron density… In Coot I get no ligand with “Find ligand” even when I reduce the cluster sigma level to 0.8. What am I missing here? Just another question, how to reduce the acceptable fit fraction in Coot “Find ligand”? Thanks for any advice, Fátima
Re: [ccp4bb] Ligand weak density in SHELXL
Dear Fatima, just a couple of things you may consider: - you can let shelxl refine the occupancy by assigning a free variable to the whole ligand - did you refine the structure anisotropically? At this resolution you certainly should. - maybe you made a mistake converting the files from refmac to shelxl, e.g. you might have used amplitudes where shelxl expects intensities or vice versa. Good luck, Tim On Mon, Jun 07, 2010 at 05:46:01PM +0100, Fatima Fonseca wrote: Dear all, I solved the structure of an enzyme at resolution of 1.1A with a bound substrate using Refmac5 and Coot for refinement/building. I have a very nice density for my ligand and a very good structure, as judged by Molprobity analysis. Now I'm using SHELXL to finish refinement but most of the density for my ligand disappears when I put it in, and it gets very high B factors. I though it could be some problem with the occupancy so I did a set of runs with different occupancies ranging from 0.2 to 1 and I got the best R factors when using 0.4/0.5 for the occupancy. However, I still have most of the ligand outside electron density… In Coot I get no ligand with “Find ligand” even when I reduce the cluster sigma level to 0.8. What am I missing here? Just another question, how to reduce the acceptable fit fraction in Coot “Find ligand”? Thanks for any advice, Fátima -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] Ligand weak density in SHELXL
Dear Tim, Thanks for your advice. I am refining my structure anisotropically. If, as you suggested, I did something wrong converting files to use in SHELXL I would expect that the whole structure to have problems or am I wrong? And how can I assign a free variable to the whole ligand? I've just started using SHELXL. Best, Fátima Em Mon, 7 Jun 2010 20:54:07 +0200 Tim Gruene t...@shelx.uni-ac.gwdg.de escreveu: Dear Fatima, just a couple of things you may consider: - you can let shelxl refine the occupancy by assigning a free variable to the whole ligand - did you refine the structure anisotropically? At this resolution you certainly should. - maybe you made a mistake converting the files from refmac to shelxl, e.g. you might have used amplitudes where shelxl expects intensities or vice versa. Good luck, Tim On Mon, Jun 07, 2010 at 05:46:01PM +0100, Fatima Fonseca wrote: Dear all, I solved the structure of an enzyme at resolution of 1.1A with a bound substrate using Refmac5 and Coot for refinement/building. I have a very nice density for my ligand and a very good structure, as judged by Molprobity analysis. Now I'm using SHELXL to finish refinement but most of the density for my ligand disappears when I put it in, and it gets very high B factors. I though it could be some problem with the occupancy so I did a set of runs with different occupancies ranging from 0.2 to 1 and I got the best R factors when using 0.4/0.5 for the occupancy. However, I still have most of the ligand outside electron density… In Coot I get no ligand with “Find ligand” even when I reduce the cluster sigma level to 0.8. What am I missing here? Just another question, how to reduce the acceptable fit fraction in Coot “Find ligand”? Thanks for any advice, Fátima -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A --- Maria Fátima da Fonseca PhD student CESAM Dep. Biologia Campus Universitário de Santiago, Universidade de Aveiro 3810-Aveiro, Portugal Fax: 234 372 587 E-mail: ffons...@ua.pt
