[phenixbb] Defining an Intermolecular link

Nigel Moriarty nwmoriarty at lbl.gov
Wed Jan 19 13:08:21 PST 2011


There is also an alpha program

elbow.ligand_linking model.pdb

that may help.


On Wed, Jan 19, 2011 at 11:13 AM, Ralf W. Grosse-Kunstleve
<rwgk at yahoo.com> wrote:
> Hi Ryan,
> Probably the easiest way to deal with your situation is to use the
> "custom bond" feature described in the phenix.refine documentation:
> https://www.phenix-online.org/documentation/refinement.htm
> See also the FAQ on pages 3 and 4 of the newsletter that just came out:
> http://www.phenix-online.org/newsletter/CCN_2011_01.pdf
> I suggest you inspect the .geo file written by phenix.refine to
> verify that the geometry restraints are processed correctly.
> Ralf
> ----- Original Message ----
>> From: Ryan Timothy Vanderlinden <r.vanderlinden at biochem.utah.edu>
>> To: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
>> Sent: Wed, January 19, 2011 9:26:25 AM
>> Subject: [phenixbb] Defining an Intermolecular link
>> Hi,
>> I am working on a complex of three molecules in which, I believe,  there is a
>>covalent bond between the sulfur atom of a cysteine on molecule "A"  and the
>>c-terminal carbon of molecule "C". There are other structures deposited  that
>>have a similar linkage. I have looked at these structures and included a
>>replica description of the supposed link in my input pdb file for refinement. I
>>have redefined this c-terminal residue as a ligand and used phenix elbow do
>>create a .cif file for it. Even when I use the modified pdb file that describes
>>the linkage and the cif file that describes the ligand, the intermolecular link
>>falls apart and the ligand (c-terminal amino acid) separates from the rest of
>>the chain. The resulting mtz file still shows density (2Fo-Fc) supporting the
>>link but the ligand is not in the density. The fact that the ligand moves away
>>from where I would expect it is evidence that modeling the intermolecular
>>linkage is really incorrect or I have not included all the proper files to
>>define this linkage and hold it together during refinement. What are all the
>>necessary files required hold an intermolecular linkage of this nature together
>>during refinement? Are there certain commands that I might be leaving out from
>>my refine script that are necessary to recognize such linkages?
>> Thanks in  advance,
>> Ryan VanderLinden
>> University of  Utah
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

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