Re: [ccp4bb] normalization of B-factor values from different crystal structures

2017-08-02 Thread James Holton
Woops, sorry. There was a typo in my response. here it is again without the typo. B factors are 78.96x the value of the mean square variation in an atom's position. The square is the important part of how you scale them. Lets say you have static disorder in the crystal lattice, and that

Re: [ccp4bb] Aimless number of uniques

2017-08-02 Thread Phil Evans
What do you mean by “unique”? In the absence of anomalous signal, I+ and I- should be the same, so are not independent, and it doesn’t make sense to count them separately. Even if there is some anomalous signal, it is generally small on average compared to the whole intensity, so I+ and I- are

Re: [ccp4bb] normalization of B-factor values from different crystal structures

2017-08-02 Thread Avinash Punekar
Hi Asmita, Try running your different crystal structures through PDB_REDO. That should normalize the B-factors to some meaningful values for comparison. Best wishes, Avinash

Re: [ccp4bb] refmac output

2017-08-02 Thread Pavel Afonine
Hi Ed, your suggestion makes perfect sense to me, and it's trivial to add an option to do what you want. This will be available in next Phenix nightly build (clearly not tomorrow given today's power outage). Command line: use "write_map_coefficients_only=True" (by default is is False).

Re: [ccp4bb] normalization of B-factor values from different crystal structures

2017-08-02 Thread James Holton
B factors are 78.96x the value of the mean square variation in an atom's position. The square is the important part of how you scale them. Lets say you have static disorder in the crystal lattice, and that gives every atom an rms variation of 0.5 A relative to their ideal lattice positions,

Re: [ccp4bb] normalization of B-factor values from different crystal structures

2017-08-02 Thread Ethan A Merritt
On Wednesday, 02 August, 2017 21:58:07 Asmita Gupta wrote: > Hi, > > Thanks for the response! > > What I have are crystal structures of the same protein in multiple > conformations, solved by different groups. I wanted to calculate the > residue-wise B-factors for each of these structures and

[ccp4bb] LBNL power outage

2017-08-02 Thread Nicholas Sauter
Dear software users, All LBNL crystallographic servers will be off line due to a power shutdown, taken as a precaution due to a nearby wild land fire in the Berkeley hills. This will affect PHENIX, LABELIT, CCTBX and other servers. We apologize for the downtime. Nick Nicholas K. Sauter, Ph.

Re: [ccp4bb] normalization of B-factor values from different crystal structures

2017-08-02 Thread Pavel Afonine
Hi, also keep in mind that the total model structure factor used in refinement and anywhere where model-to-data agreement needs to be evaluated (such as maps or R factors) is: Fmodel = ktotal * (Fcalc_atoms + F_bulk_solvent + F_something_else) where ktotal ~ scale * exp(-h*Uoverall*h_transpose)

Re: [ccp4bb] refmac output

2017-08-02 Thread Edwin Pozharski
Just to clarify, how do you use the extra columns in this scenario? My suggestion was to have the output file that includes only the map coefficient columns, so you still can look at the map. IIRC, FP/SIGFP columns from refmac output are actually modified from the input (scaled with Boverall),

Re: [ccp4bb] normalization of B-factor values from different crystal structures

2017-08-02 Thread Asmita Gupta
Hi, Thanks for the response! What I have are crystal structures of the same protein in multiple conformations, solved by different groups. I wanted to calculate the residue-wise B-factors for each of these structures and compare how the values are changing for corresponding residues in these

[ccp4bb] normalization of B-factor values from different crystal structures

2017-08-02 Thread Asmita
Hi, This might look as a very fundamental question. I have a dataset of crystal structures better than 3.5Ang resolution. For a qualitative analysis, I want to compare the residue-wise B-factors in these structures, but due to different procedures adopted in refinement and scaling, I understand

Re: [ccp4bb] refmac output

2017-08-02 Thread Ethan A Merritt
On Wednesday, 02 August, 2017 16:12:30 Edwin Pozharski wrote: > Just to clarify, how do you use the extra columns in this scenario? My > suggestion was to have the output file that includes only the map > coefficient columns, so you still can look at the map. IIRC, FP/SIGFP > columns from refmac

Re: [ccp4bb] normalization of B-factor values from different crystal structures

2017-08-02 Thread Ethan A Merritt
On Wednesday, 02 August, 2017 12:09:35 Asmita wrote: > Hi, > > This might look as a very fundamental question. I have a dataset of crystal > structures better than 3.5Ang resolution. For a qualitative analysis, I > want to compare the residue-wise B-factors in these structures, but due to >

[ccp4bb] Kendrew Symposium, 16-17 Nov 2017, EMBL Heidelberg, Germany

2017-08-02 Thread Christoph Mueller
Dear Colleagues, We would like to draw your attention to the 2-day Kendrew Symposium: "Revolutions in Structural Biology: Celebrating the 100th Anniversary of Sir John Kendrew" which will take place on 16-17 November 2017 at EMBL Heidelberg. The aim of this event is to celebrate Sir John

[ccp4bb] Experienced Research Technician in Structural Biology

2017-08-02 Thread Vidya Darbari
Dear Colleagues, I would really appreciate if you could help share the information regarding this available position for an experienced Research technician in Structural Biology. All necessary information and how to apply is in the link