Re: [phenixbb] Fitting ligand using coot

you can always do it the "old way": - place a marker atom at the centre of the ligand density and write down the coordinates - open your pdb file of the ligand with a text editor - substract/add approximate values to your ligand coordinates to fall around your marker atom - rotate, translate and real-space refine coot until the ligand is more or less correctly fitted - refine with your favourite program Quoting [email protected]:

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" :

...

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, mailto:[email protected]> 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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...................... 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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