Using Reference Structure in Phenix Refine
Hello Everyone, I am refining against low resolution data, and I would like to use a higher resolution model that is available as a reference structure. There are multiple copies of the molecule in the asymmetric unit, each with a different chain ID. Does the reference PDB file need to contain multiple copies, such that there is a match for each chain (e.g. RESIDs and SEGIDs)? Or does phenix figure out that the reference structure refers to several copies of the molecule, and you only need a single copy in the reference molecule PDB file? Or will NCS restraints take care of this? Thanks. -John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.
Hi John, Sorry for the luck of documentation on this matter. Jeff is the right person to reply to this.... I guess you need to use this to define the relationship between reference and your current model atoms: reference_model { reference_group { reference = None selection = None } } So I presume you do not need to replicate copies in your reference high resolution model, but just define the atoms in your current and reference model that should approximately match. If you have any questions or problems then please just send me the input files and I will try to figure out the best strategy to use. Or let's see what Jeff thinks about it. Pavel. On 12/4/10 11:18 AM, John Pascal wrote:
Hello Everyone,
I am refining against low resolution data, and I would like to use a higher resolution model that is available as a reference structure.
There are multiple copies of the molecule in the asymmetric unit, each with a different chain ID. Does the reference PDB file need to contain multiple copies, such that there is a match for each chain (e.g. RESIDs and SEGIDs)? Or does phenix figure out that the reference structure refers to several copies of the molecule, and you only need a single copy in the reference molecule PDB file? Or will NCS restraints take care of this?
Thanks. -John
Hi John,
For your situation you will only need one reference chain in your
reference PDB, and then you will need to add selection statements to
your parameter file to tell Phenix how you want to proceed. In the
case where your working model has four chains (A, B, C, D) and your
reference model has only chain A, the selections would look like this:
refinement.reference_model.reference_group {
reference = chain A
selection = chain A
}
refinement.reference_model.reference_group {
reference = chain A
selection = chain B
}
refinement.reference_model.reference_group {
reference = chain A
selection = chain C
}
refinement.reference_model.reference_group {
reference = chain A
selection = chain D
}
If you look at the documentation for a more recent installer, there is
more comprehensive documentation for adding a reference model that
will be included in the next release. You can find a copy here:
http://www.phenix-online.org/version_docs/dev-598/refinement.htm#anch28
If you have any further questions please let me know.
Thanks,
Jeff
On Sat, Dec 4, 2010 at 11:18 AM, John Pascal
Hello Everyone,
I am refining against low resolution data, and I would like to use a higher resolution model that is available as a reference structure.
There are multiple copies of the molecule in the asymmetric unit, each with a different chain ID. Does the reference PDB file need to contain multiple copies, such that there is a match for each chain (e.g. RESIDs and SEGIDs)? Or does phenix figure out that the reference structure refers to several copies of the molecule, and you only need a single copy in the reference molecule PDB file? Or will NCS restraints take care of this?
Thanks. -John
-- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107
---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Jeff Headd -
John Pascal -
Pavel Afonine