refinement with alternative molecules?
Hi, Recently I got a crystal structure of a multiple-molecules protein complex. There are many protein subunits with the same fold. From the likelihood-weighted maps by Phenix, I can see two different subunits occupy the same position. (So I can put the model of either subunit in the same densities, but some loop regions and the C-terminal tail look different. ). I know Phenix can do occupancy refinement with a residue that has N alternative conformations. My question is can Phenix do occupancy refinement with alternative molecules? The RMSD for two subunits is about 1.3 angstrom. The sequence identity is about 30%. Thank you very much! Su-Chang Lin, Ph.D., Postdoc Associate Department of Biochemistry Weill Medical College, Cornell University Whitney Building, room W-212 1300 York Avenue, New York, NY 10021 212-746-6458
Hi Su-Chang, yes, you can do it in phenix.refine and it is very easy. Make sure both molecules have the same chain id, and assign each molecule a different altLoc identifier, like A and B. Then everything else will be done automatically next time you feed such PDB model into phenix.refine. Please let me know if you need any help with this, have any questions or need an example. Good luck, Pavel. On 1/25/10 7:09 PM, Su-Chang Lin wrote:
Hi, Recently I got a crystal structure of a multiple-molecules protein complex. There are many protein subunits with the same fold. From the likelihood-weighted maps by Phenix, I can see two different subunits occupy the same position. (So I can put the model of either subunit in the same densities, but some loop regions and the C-terminal tail look different. ).
I know Phenix can do occupancy refinement with a residue that has N alternative conformations. My question is can Phenix do occupancy refinement with alternative molecules? The RMSD for two subunits is about 1.3 angstrom. The sequence identity is about 30%.
Thank you very much! Su-Chang Lin, Ph.D., Postdoc Associate Department of Biochemistry Weill Medical College, Cornell University Whitney Building, room W-212 1300 York Avenue, New York, NY 10021 212-746-6458 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
I just made up an example of how you can do it. The input/output files are here: http://cci.lbl.gov/~afonine/example_111/ The command is in "run" file. Of course you can run any other your custom command. Pavel. On 1/25/10 7:09 PM, Su-Chang Lin wrote:
Hi, Recently I got a crystal structure of a multiple-molecules protein complex. There are many protein subunits with the same fold. From the likelihood-weighted maps by Phenix, I can see two different subunits occupy the same position. (So I can put the model of either subunit in the same densities, but some loop regions and the C-terminal tail look different. ).
I know Phenix can do occupancy refinement with a residue that has N alternative conformations. My question is can Phenix do occupancy refinement with alternative molecules? The RMSD for two subunits is about 1.3 angstrom. The sequence identity is about 30%.
Thank you very much! Su-Chang Lin, Ph.D., Postdoc Associate Department of Biochemistry Weill Medical College, Cornell University Whitney Building, room W-212 1300 York Avenue, New York, NY 10021 212-746-6458 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Ravel, Thank you for the example. I am using phenix.refine 1.6. I tried to do occupancy refinement for the alternative molecules with ALTID. At the same time, I also want to use NCS restraints in refinement. But I got the same problem as Joe Krahn had on Wed Sep 23 12:04:31 PDT 2009: He said: "When NCS restraints contain a residue with alternate conformations, that residue gets excluded from all equivalences, even if the selections contain ALTID to avoid the redundant atoms." The error message I got is "Sorry: NCS restraints selections do not produce any pairs of matching atoms". I tried different residue numbers for the alternative molecules, still got the same error message. Turning on find_automatically for ncs gave me the same error message. Is it possible that phenix.refine thought that the residues/atoms with ALTID are different from they should be? Thanks, Su-Chang
I just made up an example of how you can do it. The input/output files
are here:
http://cci.lbl.gov/~afonine/example_111/
The command is in "run" file. Of course you can run any other your custom command.
Pavel.
Hi, Recently I got a crystal structure of a multiple-molecules
There are many protein subunits with the same fold. From the
On 1/25/10 7:09 PM, Su-Chang Lin wrote: protein complex. likelihood-weighted
maps by Phenix, I can see two different subunits occupy the same position. (So I can put the model of either subunit in the same densities, but some loop regions and the C-terminal tail look different. ).
I know Phenix can do occupancy refinement with a residue that has N
alternative conformations. My question is can Phenix do occupancy refinement with alternative molecules? The RMSD for two subunits is about 1.3 angstrom. The sequence identity is about 30%.
Thank you very much! Su-Chang Lin, Ph.D., Postdoc Associate Department of Biochemistry Weill Medical College, Cornell University Whitney Building, room W-212 1300 York Avenue, New York, NY 10021 212-746-6458 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Su-Chang,
The error message I got is "Sorry: NCS restraints selections do not produce any pairs of matching atoms".
I've not spent much attention to the combination of alternative conformations and NCS restraints. The reason is that alt. conf. are useful if you have high resolution, and NCS if you have low resolution. If your resolution is sufficiently high to support alt. conf., I figured it should be OK to refine without NCS restraints. Ralf
Hi Ralf, I see. In this case, one molecule is about 100 amino acids. The structural differences between two molecules is in the level of secondary elements (loops and helix). Though the resolution is low, I would like to see if alt. conf. helps (to know the occupancies of two molecules, not to decrease the R factors). If I can use alt. conf. and NCS at the same time, it will be great. I will try to refine the structure without NCS restraints. Thanks! Su-Chang
Hi Su-Chang,
The error message I got is "Sorry: NCS restraints selections do not produce any pairs of matching atoms".
I've not spent much attention to the combination of alternative conformations and NCS restraints. The reason is that alt. conf. are useful if you have high resolution, and NCS if you have low resolution. If your resolution is sufficiently high to support alt. conf., I figured it should be OK to refine without NCS restraints.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Su-Chang,
I will try to refine the structure without NCS restraints. I'd be interested to know how it goes, although I'm too busy to get into the NCS code right now. If the resolution is low I'd think it is better to use NCS, without alt. conf. The mismatches you saw between related molcules may be pure artifacts. But trying is better than guessing! Ralf
participants (3)
-
Pavel Afonine -
Ralf W. Grosse-Kunstleve -
Su-Chang Lin