Re: [ccp4bb] Dehydration treatments

2011-05-02 Thread Matthew BOWLER
Dear Israel, as Martin pointed out we have a device here at the ESRF/EMBL, the HC1b, that produces a stream of air with a precisely controlled RH at the sample position that we have used with some success to monitor the effects dehydration has on diffraction quality. The same device is

Re: [ccp4bb] reproducibility of protein crystals

2011-05-02 Thread Ed Pozharski
On Mon, 2011-05-02 at 15:48 +0800, anita p wrote: What are the reasons behind nonreproducibility of protein crystals? There are many possible reasons. You could start by checking you protein stock for signs of degradation and preparing it afresh. -- Hurry up before we all come back to our

Re: [ccp4bb] reproducibility of protein crystals

2011-05-02 Thread Pascal Egea
Anita, Proteolysis and oxydation are the most common alteration affecting proteins during the course of crystallization. If you have drops of the trays that yielded crystals I would run a gel on those drops and look at the aspect of protein still around in the drop. That would give you some

Re: [ccp4bb] SHELXL/ BAVERAGE

2011-05-02 Thread Fátima Fonseca
Dear George, I really appreciate your kind offer but I have just solved the problem. To all that may have the same issue in the future, I should say that in my case the problem was related to the use of SHELXPRO. I was not using it properly to transform the chains read by SHELXL (numbered)

Re: [ccp4bb] SHELXL/ BAVERAGE

2011-05-02 Thread George M. Sheldrick
Dear Fatima, Thanks. I am anyway planning to allow chain identifiers in the next version of SHELXL. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax.

Re: [ccp4bb] phenix.real_space_correlation vs overlapmap

2011-05-02 Thread Pavel Afonine
Hi Matt, I'm trying to 'measure' the density in a region of my structure by integrating the electron density there (notwithstanding errors in F000). I understand that both overlapmap and phenix.real_space_correlation compute density surrounding individual atoms for their calculations. Is

Re: [ccp4bb] phenix.real_space_correlation vs overlapmap

2011-05-02 Thread James M Holton
The CCP4 program that makes the label map you are looking for is SFALL. It can be told to make a .map file where each grid point is still a floating-point number, but instead of the usual electron density it encodes the residue number, atom number, etc. The OVERLAPMAP program knows how to

Re: [ccp4bb] phenix.real_space_correlation vs overlapmap

2011-05-02 Thread Matt Warkentin
On Mon, May 2, 2011 at 12:53 PM, Pavel Afonine pafon...@gmail.com wrote: Hi Matt, I'm trying to 'measure' the density in a region of my structure by integrating the electron density there (notwithstanding errors in F000). I understand that both overlapmap and phenix.real_space_correlation

Re: [ccp4bb] phenix.real_space_correlation vs overlapmap

2011-05-02 Thread Matt Warkentin
On Mon, May 2, 2011 at 2:18 PM, James M Holton jmhol...@lbl.gov wrote: The CCP4 program that makes the label map you are looking for is SFALL. It can be told to make a .map file where each grid point is still a floating-point number, but instead of the usual electron density it encodes the

Re: [ccp4bb] phenix.real_space_correlation vs overlapmap

2011-05-02 Thread Pavel Afonine
Hi Matt, What I want is the density 'inside' each atom in the map, so that I can make quantitative comparisons of how much stuff is present in a blob (modeled or not). that's still ambiguous...: 1) do you want a density value calculated at a point, which may be, for example, a center for an