[phenixbb] Fitting ligand using coot

VAN RAAIJ , MARK JOHAN mjvanraaij at cnb.csic.es
Sat Mar 30 14:29:15 PDT 2013


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 bsubedi at btk.fi:

> 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>
>> 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
>>
>>
>>
>>
>>
>
>
>
>
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