documents explaining parameter settings in phenix-1.7.2
Hi, I want to know, about the new Phenix-1.7.2 version, whether I can find some detailed documents explaining how to set the parameters..since there are so many options and I'm not clear their meaning..Thanks~ best, wenjie
Hi wenjie, Yes, you can always find out the latest information about parameters and how to use phenix in any of these ways: 1. In the GUI clicking on the "?" (help) symbol, which will launch the documentation as a web page. From there you can always click on "Documentation Home" which takes you to the index of all Phenix documentation 2. On the command line, typing "phenix.doc" which will do pretty much the same. 3. Anywhere, go to www.phenix-online.org and click on "full documentation" which will give you the documentation for the current version. This documentation has descriptions of all the parameters and tutorials taking you through the use of phenix. All the best, Tom T
Hi, I want to know, about the new Phenix-1.7.2 version, whether I can find some detailed documents explaining how to set the parameters..since there are so many options and I'm not clear their meaning..Thanks~ best, wenjie _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Wenjie, another approach is to tell us what you want to do and chances are that we suggest something that will work for you. From your email I am not sure I understood what exactly you are trying to achieve. Pavel On 11/30/11 6:35 PM, Ruan Wenjie wrote:
Hi, I want to know, about the new Phenix-1.7.2 version, whether I can find some detailed documents explaining how to set the parameters..since there are so many options and I'm not clear their meaning..Thanks~ best, wenjie
Thank you Thomas and Pavel! I just want to know the details about the
parameter setting so that I may have better results in future.
Actually it already worked quite fine for me so far.
best,
wenjie
2011/12/1 Pavel Afonine
Hi Wenjie,
another approach is to tell us what you want to do and chances are that we suggest something that will work for you.
From your email I am not sure I understood what exactly you are trying to achieve.
Pavel
On 11/30/11 6:35 PM, Ruan Wenjie wrote:
Hi, I want to know, about the new Phenix-1.7.2 version, whether I can find some detailed documents explaining how to set the parameters..since there are so many options and I'm not clear their meaning..Thanks~ best, wenjie
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Dr. Wenjie Ruan Fudan University Handan Road 220, Shanghai P.R.China
Hi All, Will you please tell me the acceptable clashscore analyzed by MolProbity?And any suggestions to reduce rotamer outliers? Cheers, Dialing
You just need to do lots of rebuilding. I look at any clashscore above 0.7 first. For rotamer outliers, try all the rotamers suggested by Coot. Sometimes you have to adjust the backbone to fit the correct rotamer into density. Tim On Dec 2, 2011, at 6:21 AM, Dialing Pretty wrote:
Hi All,
Will you please tell me the acceptable clashscore analyzed by MolProbity?And any suggestions to reduce rotamer outliers?
Cheers,
Dialing
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Dear All, After coot rebuid,Igot a protein 3-D structure, and Phenix comprehensive validation demonstrated it is almost acceptable.Then I did the Phenix refinement , and I select all the strategies which suitable for my resolution, all the restraints and weights (default choice) suitable for my resolution, all the other options suitable for me. I optimized it 10 rounds.However after I got the PDB output file and the mtz output file after refinment, analysis by Phenix comprehensive validation demonstrated the quality of the quality of the protein 3-D structure has been lowered significantly, which makes it unacceptable. Will you please tell me how to process my refinement? In Phenix refine, which kinds of combination of strategy combination are allowable, which are not allowable, which kinds of combination of restraints and weight combination are allowable, which are not allowable, which kinds of combinations of option are allowable, which are not allowable, and why? I am looking forward to getting your reply. Cheers, Dialing
On Fri, Dec 2, 2011 at 3:36 PM, Dialing Pretty
After coot rebuid,Igot a protein 3-D structure, and Phenix comprehensive validation demonstrated it is almost acceptable.Then I did the Phenix refinement , and I select all the strategies which suitable for my resolution, all the restraints and weights (default choice) suitable for my resolution, all the other options suitable for me. I optimized it 10 rounds.However after I got the PDB output file and the mtz output file after refinment, analysis by Phenix comprehensive validation demonstrated the quality of the quality of the protein 3-D structure has been lowered significantly, which makes it unacceptable.
What are the RMS(bonds) and RMS(angles), and which version are you using? You probably just need to optimize the X-ray/stereochemistry weight - there is an option for this in the second tab in the GUI (or on the command line, optimize_xyz_weight=True).
Will you please tell me how to process my refinement? In Phenix refine, which kinds of combination of strategy combination are allowable, which are not allowable, which kinds of combination of restraints and weight combination are allowable, which are not allowable, which kinds of combinations of option are allowable, which are not allowable, and why?
For strategies, the main restriction is on overlapping atom selections for group_adp and individual_adp, plus if you are refining individual anisotropic ADPs for any atoms, these may not be part of any TLS group. Several of the other methods (such as rotamer correction) may not be compatible with twinned refinement (it's a bug, sorry). You probably shouldn't use both types of simulated annealing at once. There are many other empirical rules that are dependent on resolution and structure quality, which we don't have a good summary for yet. There is also an incomplete list of frequently asked refinement questions here: https://www.phenix-online.org/version_docs/1.7.3-924/refine_faq.htm If you email the log file to [email protected], we may have suggestions more tailored to your particular situation. (You should send it to that address, not the phenixbb, since it may contain revealing information about your structure.) -Nat
Hi,
Will you please tell me how to process my refinement? In Phenix refine, which kinds of combination of strategy combination are allowable, which are not allowable, which kinds of combination of restraints and weight combination are allowable, which are not allowable, which kinds of combinations of option are allowable, which are not allowable, and why?
your questions show me that you may need to glance through the content of these links, that summarize what crystallographic structure refinement is and how it works: - general: http://phenix-online.org/presentations/latest/pavel_refinement_general.pdf - phenix.refine specific: http://phenix-online.org/presentations/latest/pavel_phenix_refine.pdf Normally, that should answer the questions like "which parameters to refine and how". If you send a more specific question I will try to come up with a more specific answer. Pavel
participants (6)
-
Dialing Pretty -
Nathaniel Echols -
Pavel Afonine -
Ruan Wenjie -
Thomas C. Terwilliger -
Timothy Springer