Refinement Strategy vs. R gap
Hello phenixers, I am refining a liganded structure at 2.1 and I am pretty far into my modeling. Rfree = .265 rwork= .20 My asu has 399 residues one prosthetic group (3178 atoms) and 236 HOH. I just want to do one last refinement round before submission and I am not sure about the strategy I should select as I am running into the following: I- If I refine individuals sites and real space (XYZ) and individual ADP with aniso/iso selection automatic my Rfree goes up slightly and Rwork drops to about .196. I also select optimize x-ray/ADp weight I should say. II- When I choose no XYZ refinement with anisotropic ADP for protein chain only with weight optimization Rwork plummets to 0.15 and Rfree also drops to 0.25. But my gap is now .10 !! I checked my log file and it looks like in default automatic individual ADP phenix.refine is picking all the residues to be anisotropic even though I would not try that at 2.1 A. Could someone point me in the right direction, there is probably something I am overlooking. Thank you -- Yuri Pompeu
On Wed, Mar 16, 2011 at 11:10 AM, Yuri
I am refining a liganded structure at 2.1 and I am pretty far into my modeling. Rfree = .265 rwork= .20
Not great, but not awful.
II- When I choose no XYZ refinement with anisotropic ADP for protein chain only with weight optimization Rwork plummets to 0.15 and Rfree also drops to 0.25. But my gap is now .10 !!
You shouldn't be refining any individual ADPs as anisotropic at this resolution - except perhaps metal ions. Use TLS groups instead; this often has the effect of reducing the R-free/R-work gap. (Note that phenix.refine will still output ANISOU records for all atoms in TLS groups, but they won't be individually refined.)
I checked my log file and it looks like in default automatic individual ADP phenix.refine is picking all the residues to be anisotropic even though I would not try that at 2.1 A.
That seems unlikely - can you send the logfile to [email protected] (*not* the list)? -Nat
Nat, I checked the log file and it looks like it picked residues to be anisotropic, but when I re-ran it with the automatic selection it did not. Sometimes I have to exit out and re open the GUI so it picks up on changes. On a different note, I am having trouble running TLS. After I find the optimal number of groups (either through phenix or TLSMD server) my selection shows up on the GUI but there is no button that lets me close that window to move on with the refinement. The only way to close that window is by hitting Cancel, clearly not what we want... If I dont close the window, phenix.refine says I am still editing TLS params and will not start obviously. any light? -- Yuri Pompeu
On Wed, Mar 16, 2011 at 1:19 PM, Yuri
I checked the log file and it looks like it picked residues to be anisotropic, but when I re-ran it with the automatic selection it did not. Sometimes I have to exit out and re open the GUI so it picks up on changes.
That sounds like a bug. Can you send me the parameter files and log files?
On a different note, I am having trouble running TLS. After I find the optimal number of groups (either through phenix or TLSMD server) my selection shows up on the GUI but there is no button that lets me close that window to move on with the refinement. The only way to close that window is by hitting Cancel, clearly not what we want... If I dont close the window, phenix.refine says I am still editing TLS params and will not start obviously.
Definitely a bug - it is fixed in the nightly builds, but I will send you the patch for 1.7. However, the "Update and exit" button on the toolbar (green checkmark) closes the window. (So does the cancel button.) -Nat
Hi Yuri,
I am refining a liganded structure at 2.1 and I am pretty far into my modeling. Rfree = .265 rwork= .20
did you do Xray target/Restraints weights optimization for both: coordinates and ADP refinement?
I- If I refine individuals sites and real space (XYZ) and individual ADP with aniso/iso selection automatic my Rfree goes up slightly and Rwork drops to about .196. I also select optimize x-ray/ADp weight I should say.
If this is happening after a phenix.refine with Xray target/Restraints weights optimization for both: coordinates and ADP refinement, then 1) make sure you are using the very latest PHENIX version from nightly builds; 2) if you are using the latest version, then you can set weights manually such that it results in smaller gap between Rfree/Rwork.
II- When I choose no XYZ refinement with anisotropic ADP for protein chain only with weight optimization Rwork plummets to 0.15 and Rfree also drops to 0.25. But my gap is now .10 !!
You can't refine individual anisotropic ADPs at 2.1A (if this is what you did), so the result you got is quite expected.
I checked my log file and it looks like in default automatic individual ADP phenix.refine is picking all the residues to be anisotropic even though I would not try that at 2.1 A.
phenix.refine does not do it, unless you ask it to do. I'm confused at this point about what you have done. If you send me the data and model files, as well as any CIF files for ligands (if any), then I will send you back the most optimal refinement strategy for your specific case. Pavel.
participants (3)
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Nathaniel Echols -
Pavel Afonine -
Yuri