Re: [ccp4bb] paired refinement

[Eric Karg]

Thank you for all your comments! I think it would be great to have the "paired 
refinement" implemented in future updates of refinement programs. 

Coming back to my original questions: if I have overestimated the high 
resolution cutoff, what is the correct procedure to refine against lower 
resolution data? Reprocessing the data from images to a lower 
resolution(xds..), truncating at the scaling step (aimless...) or setting the 
cutoff during refinement (phenix...)? How do I have to treat Rfree flags?

Thanks!

[ccp4bb] paired refinement

[Eric Karg]

Hi all,

I have a dataset processed in XDS to 2.3 A (based on CC1/2). I'm trying to do 
"paired refinement" to determine the optimal resolution cutoff. Here is what I 
get at different resolutions set in Phenix:

Final Rfree/Rwork:
2.7—> 0.2498/0.2027
2.6—> 0.2519/0.2009
2.5—> 0.2567/0.2025
2.4 —> 0.2481/0.2042
2.3 —> 0.2493/0.2075

The geometry of all output structures are similar.

1. What is the high resolution cutoff based on these data? I know that 
Rfree/Rwork at different resolution should not be compared, but is there a 
simple way to do the test as described in the K&D 2012 Science paper using 
Phenix GUI?

2. For refining a structure at a lower resolution (lower than the initial 
dataset), do I simply set the resolution limit in the refinement or I need to 
reprocess the data starting from the images? Do I need to do anything with 
Rfree flags? Based on the discussions on this forum I know I should deposit the 
highest resolution dataset but my question is about the mtz file which will be 
used for refinement. 

Thank you very much for your help!

[ccp4bb] Low Phaser RFZ

[Eric Karg]

Hi all,

Running Phaser using the apo protein as search model on a ~2.5 A dataset of a 
protein-DNA complex, I get a single solution but with low RFZ. The map looks 
reasonable but I was wondering why the RFZ is so low. Would this solution be 
acceptable?

   SOLU SET  RFZ=3.2 TFZ=8.4 PAK=0 LLG=66 TFZ==10.6 RFZ=2.9 TFZ=13.7 PAK=0 
LLG=203
TFZ==14.0 LLG=1440 TFZ==34.2
   SOLU SPAC P 62 2 2
   SOLU 6DIM ENSE ensemble1 EULER 181.8 55.7 74.8 FRAC 0.27 0.26 -0.40 BFAC 
-7.38
   SOLU 6DIM ENSE ensemble1 EULER 4.5 120.2 7.9 FRAC -0.31 0.20 -0.09 BFAC 12.61
   Ensemble ensemble1 RMS variance(s): 0.87

Thank you for your help!

Re: [ccp4bb] COOT library

[Eric Karg]

Thanks Huw. Unfortunately I have the same problem when using the new libraries. 
Maybe it has something to do with the pdb file (output from Phaser) I'm trying 
to refine. Do I have to rename the residues in the pdb file or is there another 
trick?

Re: [ccp4bb] COOT library

[Eric Karg]

Thanks for the suggestions. I could solve the problem by using the setenv 
command to the coot directory,but I still cannot use the Real Space Refine Zone 
in Coot because the names are not compatible. I'm trying to build an RNA 
molecule by the way.

Any suggestions?

Eric

[ccp4bb] COOT library

[Eric Karg]

Dear all,

Is there a way to make COOT use it's own libraries and not the ones from ccp4 
which is the default? I've tried using the command export 
COOT_REFMAC_LIB_DIR=//path/to/coot//share/coot/lib (mentioned elsewhere) but it 
doesn't work.

Thanks

Eric

[ccp4bb] MOLREP no output!

[Eric Karg]

Dear all,

I'm using MOLREP in CCP4 for MR. The problem is that it doesn't output a pdb 
file although the last contrast value written in the log file is 3.13! Are 
there certain criteria which have to be fulfilled before it gives a pdb file or 
is it a bug?

Thanks for your help!

Eric