[phenixbb] Fitting ligand using coot

bsubedi at btk.fi bsubedi at btk.fi
Sat Mar 30 13:42:35 PDT 2013


Dear Jurgen,

Its the second case (b). I selected the difference density as well. I tried
every option but the coot complains no ligand found and asks to adjust r.m.s.d.
Further, I have transfered rfree flag from the previous structure that has no
ligand bound. Could it be the reason? As stated earlier I can see the density
for the ligand. Also, I tried "Ligandfit" and "ligandidentifier" in PHENIX.
They too failed.

Best regards,

Bishwa


 Quoting "Bosch, Juergen" <jubosch at jhsph.edu>:

> Just to clarify, with coot do not identify the ligand you mean
>
> a) your ligand could not be read by coot
> b) Coot did not place it anywhere ?
>
> if a, then run phenix.elbow to fix your ligand
> If b, then select to difference density map as the map where the ligand is
> supposed to be found
>
> Hope that helps,
>
> Jürgen
> ......................
> Jürgen Bosch
> Johns Hopkins University
> Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology
> Johns Hopkins Malaria Research Institute
> 615 North Wolfe Street, W8708
> Baltimore, MD 21205
> Office: +1-410-614-4742
> Lab:      +1-410-614-4894
> Fax:      +1-410-955-2926
> http://lupo.jhsph.edu
>
> On Mar 30, 2013, at 3:58 PM, <bsubedi at btk.fi<mailto:bsubedi at btk.fi>> wrote:
>
> Hi all,
>
> I tried to fit the ligand using the coot -> calculate-> other modeling
> tools->
> Find ligands. I have imported cif to coot and also opened the pdb file of my
> ligand. However, coot do not identify the ligand and asks to adjust r.m.s.d.
> I
> can see the density for my ligand. Could anyone suggest me what could be the
> problem or if I am missing anything here.
>
> Best regards.
>
> Bishwa
>
>
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> phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
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>
> ......................
> Jürgen Bosch
> Johns Hopkins University
> Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology
> Johns Hopkins Malaria Research Institute
> 615 North Wolfe Street, W8708
> Baltimore, MD 21205
> Office: +1-410-614-4742
> Lab:      +1-410-614-4894
> Fax:      +1-410-955-2926
> http://lupo.jhsph.edu
>
>
>
>
>






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