[phenixbb] Fitting ligand using coot

Bosch, Juergen jubosch at jhsph.edu
Sat Mar 30 13:46:25 PDT 2013


try reducing the sigma level of the density to fit to, try perhaps 2.5 sigma

Jürgen

On Mar 30, 2013, at 4:42 PM, <bsubedi at btk.fi<mailto:bsubedi at btk.fi>> wrote:

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<mailto: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><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


_______________________________________________
phenixbb mailing list
phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org><mailto:phenixbb at phenix-online.org>
http://phenix-online.org/mailman/listinfo/phenixbb

......................
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









_______________________________________________
phenixbb mailing list
phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
http://phenix-online.org/mailman/listinfo/phenixbb

......................
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




-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20130330/cbd04e16/attachment.htm>


More information about the phenixbb mailing list