Re: [ccp4bb] Model refinement problems when upgrading Phenix

2020-07-21 Thread Phil Jeffrey
Hello Juan First, there's a phenix.refine bulletin board, on which you might attract the attention of the developers, which might help. http://www.phenix-online.org/mailman/listinfo/phenixbb I've been using 1.17-3644 without issues after transitioning from something older. Consider downgradi

[ccp4bb] Model refinement problems when upgrading Phenix

2020-07-21 Thread JUAN ESTEVEZ GALLEGO
Dear all, I have been working on the refinement of a crystal structure using phenix.refine from the 1.12-2828-Intel-Linux-2.6 version of Phenix. I have recently replaced my computer by a MacBook and I have upgraded Phenix to the 1.18.2-3874-MacOs version. However, I found that the refineme

Re: [ccp4bb] model refinement (corrections, apologies!)

2010-06-24 Thread Eleanor Dodson
Rfactors can vary a lot for equally good results it seems. You need to look at your Rfactor v resolution to see if there are any problems - ice rings? low resolution stuff? etc etc Have you used TLS sensibly - this can help.. etc etc But if the maplooks good you should be happy. Eleanor Tim G

Re: [ccp4bb] model refinement (corrections, apologies!)

2010-06-18 Thread Pavel Afonine
Hi Atul, On Fri, Jun 18, 2010 at 09:14:28AM +, atul kumar wrote: Dear all [...] these. Other than that, there are no major issues. I was just wondering if the present R-factor values seem alright for a 1.9 ang data, which many of you have suggested it does? Atul the typical R-facto

Re: [ccp4bb] model refinement

2010-06-18 Thread Clayton, Gina Martyn
! Gina From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of atul kumar Sent: Friday, June 18, 2010 5:14 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] model refinement (corrections, apologies!) Dear all Thanks for your replies. And thanks to

Re: [ccp4bb] model refinement (corrections, apologies!)

2010-06-18 Thread Tim Gruene
On Fri, Jun 18, 2010 at 09:14:28AM +, atul kumar wrote: > Dear all > > [...] these. Other than that, there are no major issues. I was just > wondering if the present R-factor values seem alright for a 1.9 ang data, > which many of you have suggested it does? > > Atul Yes, it does. The R-val

Re: [ccp4bb] model refinement (corrections, apologies!)

2010-06-18 Thread Flip Hoedemaeker
Hi Atul, With an I/sig of 2.3 and 99.9% completeness in the highest resolution shell you could have collected to an even higher resolution it would seem That might help in modeling the solvent molecules. Do you have more crystals? Flip atul kumar wrote: Dear all Thanks for your replie

Re: [ccp4bb] model refinement (corrections, apologies!)

2010-06-18 Thread atul kumar
Dear all Thanks for your replies. And thanks to all those who noticed that I had posted wrong unit cell dimensions for P3221 (which I picked from the header of the template pdb). My space group is P3221 (unit cell 54.8 54.8 100.1 90 90 120). Data quality appears fine. I/sigI=4.9; Rmerge=0.088;

[ccp4bb] model refinement

2010-06-18 Thread atul kumar
Dear all I am trying to solve structure of data set at 1.9 A,r merge 9.3,it belongs to space group P3221 unit cell 160.78 157.32 135.62 90.0 90.0 90.0,i has no NCS ,i did tls refinement as well but after water addition the r factor and r free is stucked at 22 and 25 respectively.suggestions are req