Can't you just delete your ligand from the pdb file? Jacob On Fri, Jun 3, 2011 at 10:41 AM, Desi Mail wrote:

But the 2Fo map around the ligand without omit is well defined. Phenix defines a very big box around the target pdb-includes surrounding protein residues. Is there a way to control this?

The omit map of the water molecule in the binding site is also poor.

Thanks

On Fri, Jun 3, 2011 at 10:37 AM, Ed Pozharski wrote:

...

On Fri, 2011-06-03 at 10:21 -0400, Desi Mail wrote:

...

But the 2Fo density around the ligand is very poor.

perhaps your ligand is disordered

-- "Hurry up before we all come back to our senses!"                           Julian, King of Lemurs

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: [email protected] *******************************************

On Fri, 2011-06-03 at 11:41 -0400, Desi Mail wrote:

But the 2Fo map around the ligand without omit is well defined. Phenix defines a very big box around the target pdb-includes surrounding protein residues. Is there a way to control this?

The omit map of the water molecule in the binding site is also poor.

BTW, do you mean 2Fo-Fc map, not 2Fo? And what exactly you mean by poor density? Don't know if the box size can be changed, but if you want to omit just the ligand, follow Jacob's suggestion - omit the ligand and run simulated annealing to remove bias. In theory, the observed behavior suggests model bias. What's the resolution? -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs

You may want to adjust contouring level On Fri, 2011-06-03 at 13:23 -0400, Mary wrote:

Yes. It is 2Fo-Fc map. The resolution is 1.36 with 97% completeness. I have attached three small screen shots to clarify your suggestions. lig density-ref11.tif- 2Fo-Fc map before ligand fitting lig omit density.tif - map after omitting the ligand from the final pdb. density-no lig.tif - map without the ligand using the final pdb

Thanks Mary

On Fri, Jun 3, 2011 at 12:47 PM, Ed Pozharski wrote: On Fri, 2011-06-03 at 11:41 -0400, Desi Mail wrote: > But the 2Fo map around the ligand without omit is well defined. > Phenix defines a very big box around the target pdb-includes > surrounding protein residues. Is there a way to control this? > > The omit map of the water molecule in the binding site is also poor. >

BTW, do you mean 2Fo-Fc map, not 2Fo? And what exactly you mean by poor density?

Don't know if the box size can be changed, but if you want to omit just the ligand, follow Jacob's suggestion - omit the ligand and run simulated annealing to remove bias.

In theory, the observed behavior suggests model bias. What's the resolution?

-- "I'd jump in myself, if I weren't so good at whistling."

Julian, King of Lemurs

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /