Raj In the more recent versions of PHENIX, phenix.refine can found and link atoms closer than 3 angstrom if you specify intra_chain=True. In the older versions, you can use phenix.ligand_linking to generate the needed files. Nigel PS PHENIX does not read SSBOND or LINK records but there is a script to generate the link files from the LINK records. On Tue, Feb 12, 2013 at 11:56 PM, Sabine Schneider < [email protected]> wrote:

Hello Raj,

do you have the link specified in you PDB file? Here is an example for an disulphide bond. Usually the link is the line above the CRYST1 card.

SSBOND 1 CYS A 123 CYS A 123 1555 8555 2.12

Best, Sabine

On 02/12/2013 11:21 PM, Rajeshwer Sankhala wrote:

Hello,

I can see additional density just next to Cys residues in my protein structure and it looks like BME is covalently linked to cys. I could form a disulfide bond between BME and Cys in "Refmac 5 review restrain" but when i subject it for refinement BME is thrown away (no disulfide bond). I also given Cif file in refinement but it didnot help. I have a feel that i am missing something in cif file. Can anyone suggest step by step starting from adding BME to making a link with BME (Cys-BME) and then refinement?

Raj

_______________________________________________ phenixbb mailing [email protected]http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

That will work also. On Wed, Feb 13, 2013 at 2:34 PM, Abhinav Kumar wrote:

How about using residue CME which is the CYS and BME linked together. CME is included in the CCP4 monomer library, and so Phenix should accept it without a dictionary file.

Thanks, Abhinav

JCSG@SSRL, SLAC (650) 926-2992 On 02/13/2013 01:02 PM, Nigel Moriarty wrote:

Raj

In the more recent versions of PHENIX, phenix.refine can found and link atoms closer than 3 angstrom if you specify intra_chain=True. In the older versions, you can use phenix.ligand_linking to generate the needed files.

Nigel

PS PHENIX does not read SSBOND or LINK records but there is a script to generate the link files from the LINK records.

On Tue, Feb 12, 2013 at 11:56 PM, Sabine Schneider < [email protected]> wrote:

...

Hello Raj,

do you have the link specified in you PDB file? Here is an example for an disulphide bond. Usually the link is the line above the CRYST1 card.

SSBOND 1 CYS A 123 CYS A 123 1555 8555 2.12

Best, Sabine

On 02/12/2013 11:21 PM, Rajeshwer Sankhala wrote:

Hello,

I can see additional density just next to Cys residues in my protein structure and it looks like BME is covalently linked to cys. I could form a disulfide bond between BME and Cys in "Refmac 5 review restrain" but when i subject it for refinement BME is thrown away (no disulfide bond). I also given Cif file in refinement but it didnot help. I have a feel that i am missing something in cif file. Can anyone suggest step by step starting from adding BME to making a link with BME (Cys-BME) and then refinement?

Raj

_______________________________________________ phenixbb mailing [email protected]http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov