[ccp4bb] refmac5, SIGF/SIGIMEAN labels

Hi all, we noticed a strange behaviour of refmac5.7.0029 that comes with CCP4-6.3. We run a most basic script: 5 rounds of restrained refinement with all default parameters. The input mtz file contains besides H/K/L and FreeR_flag, IMEAN/SIGIMEAN, and F/SIGF. Refmac 5.6.0117 outputs F/SIGF,

[ccp4bb] Alternative conformation of Phe and Tyr?

Dear ccp4bb, I am working on refinement of an enzyme structure. I notice an alternative conformation (gauche+ and gauche-) on both residues Phe and Tyr. Here is the image of electron density before refinement. Based on the different map intensity, I am quite sure there is an alternative

Re: [ccp4bb] ADP binds to the protein in solution but not show up in the structure

Dear Ni Shi, Did you test a crystal, or uncrystallized protein? It may be that due to crystal packing effects, only protein without ADP crystallizes. Best regards, Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ni shi

Re: [ccp4bb] Alternative conformation of Phe and Tyr?

Dear Ngo, What do you mean by no positive map? If you mean the green difference map density, this should go away if the refinement program did its job properly. The residual green density at the Tyr is probably due to the fact that when the Tyr is not at this position, something else (e.g.

Re: [ccp4bb] refmac5, SIGF/SIGIMEAN labels

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jan, could you attach or include the refmac script, please? Cheers, Tim On 07/27/12 08:10, Jan Abendroth wrote: Hi all, we noticed a strange behaviour of refmac5.7.0029 that comes with CCP4-6.3. We run a most basic script: 5 rounds of

Re: [ccp4bb] Alternative conformation of Phe and Tyr?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ngo Duc Tri, I would manually set the occupancy of chain A to about 30% and chain B's to 70% and try again.There is density for chain A present in the second picture, it is just weaker. Cheers, Tim On 07/27/12 10:01, Tri Ngo wrote: Dear

Re: [ccp4bb] Alternative conformation of Phe and Tyr?

Or refine the occupancies with Refmac... Roberto From my iPhone On 27 Jul 2012, at 11:04, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ngo Duc Tri, I would manually set the occupancy of chain A to about 30% and chain B's to 70% and try

Re: [ccp4bb] refmac5, SIGF/SIGIMEAN labels

Not here. SIGF is in the mtz output from refmac 5.7.029 is right below F: 4 NONE0.032.0 0 100.0016.0316.03 117.37 1.90 I FreeR_flag 5 NONE 20.0 11667.8 12429 96.42 805.15 805.15 117.37 1.90 F F 6 NONE8.6 311.4 12429 96.4288.74

Re: [ccp4bb] Alternative conformation of Phe and Tyr?

Don't forget you will need to adjust the contour level to see something with occupancy 0.3 - easily done with coot eleanor On 27 Jul 2012, at 11:25, Steiner, Roberto wrote: Or refine the occupancies with Refmac... Roberto From my iPhone On 27 Jul 2012, at 11:04, Tim Gruene

Re: [ccp4bb] Alternative conformation of Phe and Tyr?

Hi, you can't expect to see something with occupancy ~0.3 at the same cutoff level as you use to see fully occupied sites. So most likely the solution is to use a lower cutoff levels, as many suggested already. Two maps you attached look totally expectable to me. Pavel On Fri, Jul 27, 2012 at

Re: [ccp4bb] ADP binds to the protein in solution but not show up in the structure

Or similarly, the conditions in the crystallization drop (pH, ions, etc.) may kick out the ligand. JPK On Fri, Jul 27, 2012 at 3:34 AM, herman.schreu...@sanofi.com wrote: ** Dear Ni Shi, Did you test a crystal, or uncrystallized protein? It may be that due to crystal packing effects, only

[ccp4bb] Space group R32 and H32

Dear all I have a confusion on the space group R32 and H32. For a cell parameter of a = b not equal to c, alpha=beta, not equal to gamma, is it considered as R32 or H32? I tried searching the mail list archives but it does not help a beginner crystallographer like me. I also have another

Re: [ccp4bb] Space group R32 and H32

H32 indicates the hexagonal obverse setting (as you list) for a R centered trigonal cell, which is 3x larger than the primitive R32 cell indexed a=b=c, al=be=ga 90. Standard imho is the H32 setting, for which I will probably get flamed. The relation between H and R cells is depicted here:

Re: [ccp4bb] Space group R32 and H32

Hi Just to clarify - for H32, a=bc (though you could have a=b=c within measurement error), alpha=beta=90º, gamma=120º. Just having alpha=beta gamma is necessary but not sufficient. BTW, there's nothing wrong with alpha=beta=gamma=90º for the R setting. It's just not required. Sorry if

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Re: [ccp4bb] Space group R32 and H32

To add a little more clarity to the discussion. The hexagonal obverse setting is 3X larger because it is triply primitive. This means there are 3 lattice points per unit cell, similar to the face or body centered lattices, which have two lattice points per cell. To read BR's scripts: For the

Re: [ccp4bb] Space group R32 and H32

Thanks for the translation, and a correction of the translator: similar to the face or body centered lattices, which have two lattice points per cell. Is this so? Ortho F and FCC have 4 Bravais vectors All (in full translation) in chapter 5 of BMC. BR

Re: [ccp4bb] Space group R32 and H32

You are correct, sir. It is one lattice point for each centered face. So, for the F centered lattices which have a face centered lattice point on all faces you add 3 lattice points to the original primitive lattice point for a total of 4 lattice points. It's all in the Tables. Cheers, Chris