text output for model quality and validation report at phenix
Hi all, I will greatly appreciate the answers to following query: How can I get the text or excel output of the model quality and validation report of a model after phenix refinement? I am specially interested in real space CC of the various residues. I am using phenix.refine_gui at phenix-1.4-162. I have searched all output files, but couldn't find. Thanks in advance. Ravi Ravindra D. Makde, PhD Postdoctoral fellow, Tan lab, The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 USA
On Jan 4, 2010, at 10:46 AM, Ravindra D. Makde wrote:
I will greatly appreciate the answers to following query:
How can I get the text or excel output of the model quality and validation report of a model after phenix refinement? I am specially interested in real space CC of the various residues. I am using phenix.refine_gui at phenix-1.4-162. I have searched all output files, but couldn't find.
To start with, please update to at least 1.5-2. I'm not sure if 1.5-2 includes the text dump, but in the most recent installers there is a file named something like "refine_1-info.txt" that contains lists of all outliers (geometry and RSCC). However, it won't show anything other than outliers, which are fixed at CC < 0.7 (for the RSCC) or deviation > 4sigma (for geometry). It's not difficult to add user preferences for these (and complete listings of RSCCs), so I'll see if I can get this into the next build (sometime this week). ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
Hi Ravi, to get a plain text list of map CC computed per residue or per each atom you can use one of these two command line tools: phenix.model_vs_data model.pdb data.hkl or (if you want to have more options and flexibility), type: phenix.real_space_correlation hit Enter, and then follow the instructions. Note, in both options, in addition to getting map CC you will also get 2mFo-DFc and mFo-DFc printed for each atom or residue. These are very useful map quality measures that are complimentary to map CC. Example: sometime even a very weak density, say at sigma 0.1, can produce a high map CC, and if you just look at map CC you will miss it. So, I believe it is useful to look at triplets (CC, 2mFo-DFc, mFo-DFc) for each atom or residue, and this is what the above tools give you. Of course, you get it from GUI as well. Pavel. On 1/4/10 10:46 AM, Ravindra D. Makde wrote:
Hi all,
I will greatly appreciate the answers to following query:
How can I get the text or excel output of the model quality and validation report of a model after phenix refinement? I am specially interested in real space CC of the various residues. I am using phenix.refine_gui at phenix-1.4-162. I have searched all output files, but couldn't find.
Thanks in advance.
Ravi
participants (3)
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Nathaniel Echols -
Pavel Afonine -
Ravindra D. Makde