[phenixbb] Fw: on phenix.real_space_refine
pafonine at lbl.gov
Sun Oct 18 10:17:27 PDT 2015
Phenix version 1.10.1 (the latest official) is the one to use, and by
design it is supposed to be superior than previous versions. Actually
this is what you confirm with your results: with 1.10.1 you get better
model (less Ramachandran plot outliers, similar other metrics) and
better model-to-map fit (CC =0.761 vs 0.687).
It is not clear to me why you find the model from 1.10.1 version
I suggest you to find a handful of most severe steric clashes and
> Today I just completed another protein phenix.real_space_refine. For
> the following comparison runs, the initial model same, the map same,
> all 5 macro_cycles default run.
> For version 1.10.1, the results were as following,
> Map CC (whole unit cell)： 0.672
> Map CC （around atoms）： 0.761
> rmsd （bonds): 0.01
> rmsd (angles): 1.55
> All-atom clahscore: 39.27
> Ramachandran outlier: 0.98%
> Ramachandran allowed: 12.71%
> Ramachandran favoured: 86.31%
> Rotamer outliers: 0.91%
> C-beta deviations: 0
> For version 1.9-1692, the results were as following,
> Map CC (whole unit cell)： 0.645
> Map CC （around atoms）： 0.687
> rmsd （bonds): 0.0071
> rmsd (angles): 1.15
> All-atom clahscore:16.88
> Ramachandran outlier: 2.00%
> Ramachandran allowed: 6.23%
> Ramachandran favoured: 91.77%
> Rotamer outliers: 0.05%
> C-beta deviations: 0
> For the version 1.10.1 phenix.real_space_refine, the most
> unacceptable was on the clashscore, the whole refine process seems did
> not care on the clashcore refine at all.
> I am looking forward to getting an explanation from you on the causes
> of the difference for phenix.real_space_refine for the 2 versions, and
> the possible strategy we can take to eliminate the difference to get
> the acceptable results.
> Best regards.
> On Friday, October 9, 2015 12:52 AM, Smith Lee
> <smith_lee123 at yahoo.com> wrote:
> Dear Pavel，
> As I have told you, I have tried phenix.real_space_refine for 2
> protein with version 1.9-1692 and version 1.10 (and 1.10.1) for many
> times, with cif or without cif, with or without annealing. The general
> feedback was that the version 1.9-1692 was much much better for the
> final analysis of the PDB given at the end of the run of the
> phenix.real_space_refine. Especially for clashing score, version
> 1.9-1692 can gave acceptable results (below 20 or around 20), but the
> clashing score given by the above 2 new versions of
> phenix.real_space_refine was very high (around 50 or 100). For
> C-beta deviations, the output by 1.9-1692 was also much better
> Before I have tried the other nightly built versions of
> phenix.real_space_ refine between version 1.9-1692 and version 1.10
> (and 1.10.1) , all I gave acceptable output analysis (something like
> the Molprobity analysis at the end of the run).
> Thus may I ask the reason you have version 1.10 (and 1.10.1)
> phenix.real_space_refine was because you have realized that the result
> given by version 1.9-1692 was too satisfactory?
> One direct concern of me was that you have recommended not to use the
> old version phenix. But I cannot get the satisfactory result with the
> new version phenix.real_space_refine.
> The other concern of me was that, I have noticed there were
> publications In Nature and Science which wrote they use
> phenix.real_space_refine to got the results in Nature and Science. The
> Phenix they used should be the versions earlier than version 1.10.
> Considering what I mentioned above, the Nature and Science results may
> be not so correct, if new version of phenix was considered as much
> better than the old version.
> Thus am I the only user who communicated with you on the high clashing
> score given by the new version of phenix？Can you give some comments
> on what I mentioned above on the high clashing score given by the new
> version phenix.real_spac_refine?
> Best regards.
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