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 Pheni

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 s

[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 subm

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"

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

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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. +49

[ccp4bb] Research Associate in X-ray Protein Crystallography of Light Induced Reactions at Imperial College London

Job Title Research Associate in X-ray Protein Crystallography of Light Induced Reactions Department/Division/Faculty Division of Molecular Biosciences, Faculty of Natural Sciences South Kensington Campus, London SW7 2AZ Closing Date 1 June 2010 (midnight GMT/BST) Fixed term for 24 months Ap

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 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 low-resolution data. But I

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Applications are being accepted for a tenure track position at the Assistant or Associate Professor level in the Department of Biology, Faculty of Science, University of Waterloo. Applicants should have a PhD and postdoctoral experience with a research record in Macromolecular X-ray Crystallogr

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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Hello all, I would appreciate it if you could distribute this flier to potential applicants. Thank you, Mark Walter Post-doctoral position: Structural Biology of Cytokine-Receptor Signaling A Post-doctoral position is available immediately to study the structure and

[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

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

Re: [ccp4bb] Mysterious Crystals?

could try reverse matrix seed On Sun, Apr 18, 2010 at 10:46 PM, tat cheung cheng 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, they were needle sh

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 solutio

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 thi

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 convent