Hi phenix users, I have two questions when using Phenix Refinement. 1. I'd like to run phenix refinement with twin data but I don't know how to define twin_law using GUI Phenix refinement module in Linux. 2. I used phenix refinement in Windows to refine a 2.3A structure. My problem is the Rfree is quite high. - I applied twin refinement + TLS + NCS and SA refinement (wxu_scale = 1) Start: r_work = 0.2149 r_free = 0.2833 bonds = 0.016 angles = 1.988 Final: r_work = 0.2029 r_free = 0.2735 bonds = 0.008 angles = 1.448 - Then I use auto-weight to optimize the Rfree. optimize_xyz_weight = True optimize_adp_weight = True wxc_scale = 0.5 wxu_scale = 1 Start: r_work = 0.2152 r_free = 0.2735 bonds = 0.008 angles = 1.322 Final: r_work = 0.2309 r_free = 0.2781 bonds = 0.003 angles = 0.848 I think the bond rmsd and angle rmsd were too small in this final refinement. Do you think it's normal or I need to try more? Thank you very much for your helpful input. Best wishes, -- * TriNgo * Structural Biology Lab School of Medicine - Sungkyunkwan University Phone: 031-299-6150 Cell: 010-7774-8210
On Wed, Jan 25, 2012 at 1:29 AM, Tri Ngo
1. I'd like to run phenix refinement with twin data but I don't know how to define twin_law using GUI Phenix refinement module in Linux.
Open the Settings menu, look for "Twinning", and there should be a "Twin law" parameter in that dialog window. In the nightly builds I think I moved this to the main window, but I'll double-check.
2. I used phenix refinement in Windows to refine a 2.3A structure. My problem is the Rfree is quite high.
- I applied twin refinement + TLS + NCS and SA refinement (wxu_scale = 1) Start: r_work = 0.2149 r_free = 0.2833 bonds = 0.016 angles = 1.988 Final: r_work = 0.2029 r_free = 0.2735 bonds = 0.008 angles = 1.448
- Then I use auto-weight to optimize the Rfree.
optimize_xyz_weight = True optimize_adp_weight = True wxc_scale = 0.5 wxu_scale = 1
Start: r_work = 0.2152 r_free = 0.2735 bonds = 0.008 angles = 1.322 Final: r_work = 0.2309 r_free = 0.2781 bonds = 0.003 angles = 0.848
I think the bond rmsd and angle rmsd were too small in this final refinement. Do you think it's normal or I need to try more? Thank you very much for your helpful input.
I've found that weight optimization does tend to lead to lower RMSDs than I'd been taught to expect; I'm not sure why this is. They aren't necessarily wrong - but this may be indicative of some other issue. Do you have NCS? TLS would also be worth trying, since it sometimes helps with overfitting. -Nat
Hi,
2. I used phenix refinement in Windows to refine a 2.3A structure. My problem is the Rfree is quite high.
- I applied twin refinement + TLS + NCS and SA refinement (wxu_scale = 1) Start: r_work = 0.2149 r_free = 0.2833 bonds = 0.016 angles = 1.988 Final: r_work = 0.2029 r_free = 0.2735 bonds = 0.008 angles = 1.448
- Then I use auto-weight to optimize the Rfree.
optimize_xyz_weight = True optimize_adp_weight = True wxc_scale = 0.5 wxu_scale = 1
Start: r_work = 0.2152 r_free = 0.2735 bonds = 0.008 angles = 1.322 Final: r_work = 0.2309 r_free = 0.2781 bonds = 0.003 angles = 0.848
I think the bond rmsd and angle rmsd were too small in this final refinement. Do you think it's normal or I need to try more? Thank you very much for your helpful input.
Numbers after weight optimization look ok to me. Data of 2.3A resolution may not be able to tell you the difference between bond lengths varying by a tiny fraction of angstrom. So what you get is dictated by the Fobs data. For more details about weight optimization see "Improved target weight optimization in phenix.refine" here: http://phenix-online.org/newsletter/ Pavel
Dear All, Will you please tell me a software to get rid of the H added by Phenix ready_set? For Phenix refine I have used the H added PDB by ready_set. Although there is the opinion on that for RCSB depositation added H is fine, but there is also the opinion for RCSB depositation added H is not necessary. Thus I need to know how to remove the added H. Best regards. Dialing
On Wed, Jan 25, 2012 at 1:27 PM, Dialing Pretty
Will you please tell me a software to get rid of the H added by Phenix ready_set?
phenix.reduce -Trim model.pdb > model_noH.pdb or phenix.pdbtools model.pdb remove="element H or element D"
For Phenix refine I have used the H added PDB by ready_set. Although there is the opinion on that for RCSB depositation added H is fine, but there is also the opinion for RCSB depositation added H is not necessary. Thus I need to know how to remove the added H.
You don't necessarily need to do anything specifically to deal with the RCSB - they may remove the hydrogens automatically (whether you want them to or not). But our opinion is that you should leave the model alone. -Nat
participants (4)
-
Dialing Pretty -
Nathaniel Echols -
Pavel Afonine -
Tri Ngo