Re: [ccp4bb] Fab:Peptide complex crystallization

Hi Christine, Just have a try. When people want to co-crystallize complexes of a protein and small molecular compounds, DMSO is often introduced into the drop, since pharmacologists like to dissolve compounds in DMSO. 2010/7/19 Harman, Christine > Hi all, > I was wondering if anyone has had an

Re: [ccp4bb] A strange case of MR

Why the Rfree value is lower than Rwork? 在 2010年7月19日 上午3:41，孙庆祥 写道： > Dear Collins and all, > > Thanks for the reply. Please find the following pdb header. For your > information, this is after refmac5 with twin-refinement option selected. > This is the best R values that I'm getting. Cutting re

[ccp4bb] Postdoctoral Position available

One postdoctoral X-ray crystallographer positions is immediately available in the group of Wolfgang Peti at Brown University (Providence, Rhode Island, USA). The person will focus on the characterization of ser/thr protein phosphatase 1 and its role in cancer and diabetes – an example of the work

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

Just adjust the scale parameters in the FFT script - mF1-nF2 option. Eleanor Armando Albert de la Cruz wrote: Does anyone have got a script to compute 3fo2fc map with CCP4? Armando El 29/07/2010, a las 23:38, Ian Tickle escribió: On Thu, Jul 29, 2010 at 8:25 PM, Pavel Afonine wrote: Speak

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

Hi Ian, You have to be careful here because believe it or not, not all programs output the same coefficients for 'minimal bias' maps, so depending on which program Hailiang is using for SF calculation/refinement he may or may not get the right answer! You are assuming the difference map coeffi

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

Thanks Ian, that makes it clear indeed! Pavel. On 7/30/10 2:12 AM, Ian Tickle wrote: Hi Pavel The expressions Fo+(Fo-Fc) and Fc+2(Fo-Fc) are obviously equal so it makes no difference whether you look at it as [half from Fo + half from (Fo-Fc)] or [2 times half from (Fo-Fc)]. But that wasn't

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

Hello, since Fred mentioned PHENIX... (...) and mtz labels are those that are provided by Phenix... and Armando was wondering about a way to compute 3fo2fc map: Does anyone have got a script to compute 3fo2fc map (...) and CCP4 solution was already suggested, I'll take the risk of letting m

[ccp4bb] Postdoc Position in Protein Biochemistry and Protein Crystallography

Postdoc Position in Protein Biochemistry and Protein Crystallography A postdoc position is available in the laboratory of Dr Georg Groth at the Institute of Plant Biochemistry at the Heinrich-Heine University Duesseldorf (Germany) in the field of plant hormone receptor biology. The responsibil

Re: [ccp4bb] MR with polysaccharide

I fitted manually the chondroitin sulfate into my complex (3c9e.pdb and 3h7d) using program coot. The chondroitin-sulfate model was used from the PDB. I used CNS for the refinement of the first structure, and phenix for the second structure. Phenix was more convenient with this ligand as it was

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

Hi Fred But then what you suggested won't work if I'm right about phenix correctly writing 2(mFo-DFc) for acentrics and (mFo-DFc) for centrics in the FOFCWT column (as does CCP4 Sigmaa in the DELFWT column), since you will get: (2mFo-DFc) + 2(mFo-DFc) = 4mFo-3DFc for acentrics mFo + (mFo-DFc)

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

Hi Ian, If you read my post carefully, and know the naming conventions, you will see that the mtz naming convention and mtz labels are those that are provided by Phenix... I was aware that there will be differences (I was assuming minor ones - in terms of map appearance) to the proper coeffi

[ccp4bb] MR with polysaccharide

Dear all, I am seeing some bulk extra denisty near my protein molecule, in a 2.7 angstrom map. The crystallization condition condition has a sulfated polysaccharide. If I want to perform a MR with this polysaccharide, in presence of the refined protein model in the cell, which program shoul

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

Apologies for extending this somewhat but I think the question I have relates to the principles Ian and others are covering. My question is what are the correct coefficients to use if refining twinned data using twin related Icalc values. In this case, shouldn't coefficients for maps be 4mFo-3

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

Hi Fred You have to be careful here because believe it or not, not all programs output the same coefficients for 'minimal bias' maps, so depending on which program Hailiang is using for SF calculation/refinement he may or may not get the right answer! You are assuming the difference map coefficie

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

Hi Pavel The expressions Fo+(Fo-Fc) and Fc+2(Fo-Fc) are obviously equal so it makes no difference whether you look at it as [half from Fo + half from (Fo-Fc)] or [2 times half from (Fo-Fc)]. But that wasn't the point I was making: I was saying that I thought the relationship between the Fourier a

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

Hi, You take the output mtz from the refinement program (let's assume it's called refine_1.mtz). Command line mode: sftools read refine_1.mtz col 1 2 3 4 # assuming the mtz contains H K L 2FOFCWT PHI2FOFCWT FOFCWT PHI2FOFCWT cal col 3FO2FCWT col 1 col 3 + set types F P F P R F write 3fo2fc.m

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

Does anyone have got a script to compute 3fo2fc map with CCP4? Armando El 29/07/2010, a las 23:38, Ian Tickle escribió: On Thu, Jul 29, 2010 at 8:25 PM, Pavel Afonine wrote: Speaking of 3fo2fc or 5fo3fc, ... etc maps (see classic works on this published 30+ years ago), I guess the main rat