Re: [ccp4bb] chiral volumes--2nd try

Berhard, Then you have to define what you mean by smallest. SHELXL uses the (ASCII) alphabetical order of the three atom names for this purpose (SHELX manual page 7-23) so that it is unambiguous (since the names are not allowed to be the same), but presumably other programs use other

Re: [ccp4bb] how to make cholesterol solution

Jerry, Steroids have a certain solubility also in ethylene glycol and PEG. You might be able to work out a crystallization strategy around this. The ethanol/PEG combination was used in: http://www.nature.com/nature/journal/v437/n7055/full/nature03923.html Enrico. Dear ALL: Sorry for

Re: [ccp4bb] how to make cholesterol solution

if you are crystallizing membrane protein here is a useful protocol from JCIPMT website follow the link http://jcimpt.scripps.edu/protocols/JCIMPT_PreparationofCHSStock.pdf in my experience even after extensive sonication i filter the buffers otherwise we found that cholestrol comes out of

Re: [ccp4bb] Mysterious Crystals?

could try reverse matrix seed On Sun, Apr 18, 2010 at 10:46 PM, tat cheung cheng theif...@yahoo.com.hk wrote: Hi all, I have got some crystals, the purified protein was in Tris buffer with 300mM NaCl for crystallization. they grew in light weight PEG, PEG400 or monomethyl ethyl PEG500,

Re: [ccp4bb] chiral volumes--2nd try

Then you have to define what you mean by smallest. Correct. A little manual reading often goes along way :-) br

[ccp4bb] The effect of the absence of various diffraction data to the electronic density

I've seen a website where there are some dynamic pictures to show the effects of the absence of various diffraction data to the electronic density, such as the changing process of the electron density as the deletion of low-resolution data. But I can't find this website now, could anyone here also

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Re: [ccp4bb] chiral volumes--2nd try

Dear Bernhard, You indeed have plenty of space to extend the margin notes on page 631! In the REFMAC monomer library that is also used by PHENIX, the sign of the chiral volume is explicitely defined for each chiral atom by _chem_comp_chir.volume_sign. For the L-aminoacids it is always defined

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Re: [ccp4bb] The effect of the absence of various diffraction data to the electronic density

On Tue, Apr 20, 2010 at 7:35 AM, 商元 shangyuan5...@gmail.com wrote: I've seen a website where there are some dynamic pictures to show the effects of the absence of various diffraction data to the electronic density, such as the changing process of the electron density as the deletion of

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Re: [ccp4bb] chiral volumes--2nd try

For CB_ILE, the chiral volume sign in the REFMAC monomer library is the same as used by SHELXL, not the opposite as stated in my last posting. Apologies! George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel.

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Re: [ccp4bb] The effect of the absence of various diffraction data to the electronic density

Sounds like you could be referring to my movies page: http://bl831.als.lbl.gov/~jamesh/movies/ -James Holton MAD Scientist 商元 wrote: I've seen a website where there are some dynamic pictures to show the effects of the absence of various diffraction data to the electronic density, such as the

Re: [ccp4bb] Proportion of MR in PDB

For once, I actually agree with Ian! I too refer to the process as molecular replacement, even if you don't run a molecular replacement program. For those who are interested in more than one opinion, other popular method used to determine the structure in the PDB that I still call MR are:

[ccp4bb] geometry problems with sugars

Hi All, My question is concerning geometry of NAGs in a glycoprotein structure. I recently solved the structure of a glycoprotein to 3 Å and modeled NAGs linked to Asn at 3 different places.  NAGs and Asn-NAG links are refined in Phenix.refine as per the Phenix dictionary. However, when

Re: [ccp4bb] chiral volumes--2nd try

Joel, Agh. I can honestly say that this explanation never occurred to me, even though it is consistent with the data (But come on, any introductory organic chem text explains the R/S rules by moving from atom 2 to 3 to 4, and not by jumping from 2 to 4...surely you would follow the

Re: [ccp4bb] geometry problems with sugars

tirumal wrote: Hi All, My question is concerning geometry of NAGs in a glycoprotein structure. Fire away... I recently solved the structure of a glycoprotein to 3 Å and modeled NAGs linked to Asn at 3 different places. NAGs and Asn-NAG links are refined in Phenix.refine as per the