Re: [ccp4bb] Refinement in half occupancy

[Matthew Chu]

Hi Bithika,

Basically, I combined the coordinates of the two different conformations of
the ligand (e.g. *ZZZ*), which modeled in Coot individually, in one pdb, and
then put A/B label in front of the residue code and set the occupancy to
0.5, e.g.

ATOM   4052  O2A*AZZZ* X1234 -42.055 -10.565 -13.483  *0.50*50.93
 O
ATOM   4053  O2A*BZZZ* X1234 -40.667 -10.029 -15.836  *0.50*59.20
 O

Kind regards,
Matt



2008/6/10 Bithika Bera [EMAIL PROTECTED]:

 Hi Matt,
Could you please pass me all advices regarding 'refine the
 ligand in half occupancy'.
 And which one is working for you.

 Thanks,
 bb


 *Matthew Chu [EMAIL PROTECTED]* wrote:

 Thank you for all the advices, I am now able to refine the ligand in half
 occupancy!

 Matt



 2008/6/10 Guillaume Marassio [EMAIL PROTECTED]:

 I'am not sure it is your problem but you can try with A and B before the
 residue number.
 Hope it will be helpfull.
 Guillaume Marassio

 Matthew Chu a écrit :

 Dear All,

 Can anyone teach me how to refine a ligand in a protein structure with
 half occupancy in refmac?
 I have tried to combine the coordinates of the two different
 conformations of that particular ligand in one pdb, after modeling in Coot
 individually, and then changed the occupancy to 0.5 for each of the
 conformation. However, I couldn't manage to refine this pdb in Refmac.
 Thanks in advance!

 Best regards,
 Matt



 
 Matthew LH Chu
 PhD Student
 School of Pharmacy and Pharmaceutical Sciences
 University of Manchester

 






 --

 
 Matthew LH Chu
 PhD Student
 School of Pharmacy and Pharmaceutical Sciences
 University of Manchester

 





-- 

Matthew LH Chu
PhD Student
School of Pharmacy and Pharmaceutical Sciences
University of Manchester

[ccp4bb] Refinement in half occupancy

[Matthew Chu]

Dear All,

Can anyone teach me how to refine a ligand in a protein structure with half
occupancy in refmac?
I have tried to combine the coordinates of the two different conformations
of that particular ligand in one pdb, after modeling in Coot individually,
and then changed the occupancy to 0.5 for each of the conformation. However,
I couldn't manage to refine this pdb in Refmac.
Thanks in advance!

Best regards,
Matt



Matthew LH Chu
PhD Student
School of Pharmacy and Pharmaceutical Sciences
University of Manchester

Re: [ccp4bb] Refinement in half occupancy

[Nian Huang]

It should be straight forward. A good example you can use is to make
an alternate conformation of a residue in coot. Then you can follow
the generated pdb to modify your ligand. Are you sure refmac won't
run? What is the error message from refmac?

Nian Huang, Ph.D.
Dept. of Biochemistry
UT Southwestern Medical Center

On Mon, Jun 9, 2008 at 5:21 PM, Matthew Chu [EMAIL PROTECTED] wrote:
 Dear All,

 Can anyone teach me how to refine a ligand in a protein structure with half
 occupancy in refmac?
 I have tried to combine the coordinates of the two different conformations
 of that particular ligand in one pdb, after modeling in Coot individually,
 and then changed the occupancy to 0.5 for each of the conformation. However,
 I couldn't manage to refine this pdb in Refmac.
 Thanks in advance!

 Best regards,
 Matt


 
 Matthew LH Chu
 PhD Student
 School of Pharmacy and Pharmaceutical Sciences
 University of Manchester