[phenixbb] Refining sucrose

Pavel Afonine pafonine at lbl.gov
Thu May 26 00:07:16 PDT 2011


in a nutshell, the problem with CIF files created by PRODRG is that 
sometimes PRODRG assigns too small sigmas  (esds), which in turn means 
that the corresponding terms in restraint targets become much larger 
than the others (since they are proportional to 1/sigma**2), and this 
results in distorting overall geometry during refinement.

So, if you do refinement using phenix.refine it is the best to use 
phenix.ready_set to obtain cif files for your ligands, or if you get 
them from elsewhere then make sure they are correct.

You can use phenix.reel to check your cif files - my recollection is 
that it will highlight bad esds.


On 5/25/11 12:09 AM, ChenTiantian wrote:
> Hi,there
> I found that the cif file of ligand from ProDRG server is not good for 
> phenix.refine.
> I always got my ligand pdb file using ProDRG, and use the refmac file 
> as the restraint file of the ligand, but I found that after running 
> the phenix.refine, the rmsANGLE is very high.
> the I followed someone's advice, using phenix.elbow to produce the 
> ligand's cif file, that really make sense, now I can easily get the 
> refinement value of the complex structure in a
> reasonable level.
> Hope it works with your structure too.
> Tiantian
> On Tue, May 24, 2011 at 3:34 PM, Priit Eek <priit.eek at gmail.com 
> <mailto:priit.eek at gmail.com>> wrote:
>     Thanks Nigel and Yuri! elbow.where_is_that_cif_file gave me the
>     right cif to use in coot. Off to fix that sucrose now...
>     Priit
>     On 23.05.2011, at 17:55, Yuri wrote:
>     > All coot needs to run its real-space refinement is a .cif file
>     as Nigel pointed out.
>     > You can also get this file from other ligand library websites
>     (proDrg, hic-cup, etc...). The only catch here is. The name of
>     your sucrose atoms must match, exactly, those in the file.
>     > Once you have such file go to the the file drop-down menu and
>     click on Import CIF dictionary in coot. That should enable to
>     rotate the rotatable bonds of your ligand
>     >
>     > --
>     > Yuri Pompeu
>     > _______________________________________________
>     > phenixbb mailing list
>     > phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>     > http://phenix-online.org/mailman/listinfo/phenixbb
>     _______________________________________________
>     phenixbb mailing list
>     phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>     http://phenix-online.org/mailman/listinfo/phenixbb
> -- 
> Drug Discovery and Design Center,
> Shanghai Institute of Materia Medica, Chinese Academy of Sciences
> Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park,
> Pudong New Area, Shanghai, 201203, P.R. China
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20110526/15507083/attachment.htm>

More information about the phenixbb mailing list