Re: [ccp4bb] Check the conformation of one important amino acid

Or Phenix. Miles On Feb 18, 2008, at 10:28 PM, Juergen Bosch wrote: Chavas Leo wrote: Dear Sun -- I want to check the conformation of one important amino acid in the structure by looking the difference density map. Should I just omit that amino acid in the refinement or should I also omi

Re: [ccp4bb] Check the conformation of one important amino acid

Chavas Leo wrote: Dear Sun -- I want to check the conformation of one important amino acid in the structure by looking the difference density map. Should I just omit that amino acid in the refinement or should I also omit its flanking amino acids? Which one is better? The real expert will

Re: [ccp4bb] Check the conformation of one important amino acid

Dear Sun -- I want to check the conformation of one important amino acid in the structure by looking the difference density map. Should I just omit that amino acid in the refinement or should I also omit its flanking amino acids? Which one is better? The real expert will talk better than

Re: [ccp4bb] PISA parameters for surface area calculation

Dear Rafael -- I am using PISA to calculate the surface interface of a homdimeric protein. Does anyone know where I can find the parameters (probe radius, atomic radii, etc) PISA uses to calculate surface area? not sure, but would that help?: http://www.ebi.ac.uk/msd-srv/prot_int/picite.ht

[ccp4bb] Check the conformation of one important amino acid

Dear All experts, I want to check the conformation of one important amino acid in the structure by looking the difference density map. Should I just omit that amino acid in the refinement or should I also omit its flanking amino acids? Which one is better? Thank you very much for you

Re: [ccp4bb] References for ligand flipping

Jon, I have not had any replies. I did hear a talk at an American Chemical Society meeting on a ligand flipping between the two estrogen receptor subtypes, but it hasn¹t been published from what I can tell. Here¹s a link to the abstract. membership.acs.org/C/COMP/pastprograms/Fall06abstracts.pdf

[ccp4bb] X-treme and Cobra

Hi all, We are preparing to replace a cryosystem on our home rotating anode. Does anyone have any insight into a comparison of the Oxford Cobra system and the Rigaku X-treme? Many thanks, Marilyn Yoder Marilyn D. Yoder Division of Cell Biology & Biophysics School of Biological Sciences Univer

[ccp4bb] PISA parameters for surface area calculation

Hi, I am using PISA to calculate the surface interface of a homdimeric protein. Does anyone know where I can find the parameters (probe radius, atomic radii, etc) PISA uses to calculate surface area? Cheers, Rafael.

Re: [ccp4bb] indexing multiple lattices

I'm not sure if it will still work with the latest Mosflm/HKL, but Untangle might also be worth looking into: http://ultr23.vub.ac.be/untangle/ Luca Luca Jovine, Ph.D. Karolinska Institutet Department of Biosciences and Nutrition Hälsov

Re: [ccp4bb] indexing multiple lattices

Is there any way to do a search of crystal orientation matrices with a known cell to find the best fit to the diffraction pattern? The data were collected on the Pilatus6M detector so I am limited to mosflm and XDS for processing. d*TREK will easily process Pilatus6M images. Both packages alwa

Re: [ccp4bb] indexing multiple lattices

Ok, Graeme basically described the way I usually do things as well. That's the beauty of a modular program like XDS and the passing of information in ASCII format. Old-fashioned, but very, very useful ;-) I've created a short page with a recipe for using XDS in that way - there might be some typos

Re: [ccp4bb] crashing-out protein eluted from Nickel column

Hi, One has to bear in mind that adsorption at high pH (above 6.5 is already high for Imac; pKa of exposed His is 6.2) leads to stronger interactions which, in turn, require stronger eluting conditions, e.g. > 200 mM imidazole (pKa ~ 7.0). I suggest lowering the pH of the adsortion buffer, e.g

Re: [ccp4bb] indexing multiple lattices

Hmm... Thinking about this it may not be too hard to do with XDS. May involve a certain amount of fiddling though. If you do the first stages of XDS processing, namely XYCORR, INIT, COLSPOT & IDXREF you will end up with a spot file (SPOT.XDS) from colspot and with indices attached from IDXREF. On

Re: [ccp4bb] indexing multiple lattices

On Mon, Feb 18, 2008 at 01:58:59PM +0100, Jason Greenwald wrote: > I have a crystal that grows with multiple lattices despite the fact > that the crystals look more or less like single crystals under the > microscope. > > With a lot of guesswork I am able to index with mosflm by carefully >

[ccp4bb] indexing multiple lattices

I have a crystal that grows with multiple lattices despite the fact that the crystals look more or less like single crystals under the microscope. With a lot of guesswork I am able to index with mosflm by carefully selecting spots that appear to be in the same lattice. Now I would like to u

Re: [ccp4bb] crashing-out protein eluted from Nickel column

Hi, I used another way to deal with this problem. You can try to elute your protein with the buffer containing 50mM EDTA (You need at least 10CV to elute completely). Then use gel filtration to remove the Ni. I applied this method with two proteins and it showed good results. Good luck! TriNgo --

Re: [ccp4bb] XDS - resolution limit

Hi Florian,m the keyword is TRUSTED_REGION (see http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#TRUSTED_REGION= and http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDS.INP in XDSwiki). HTH, Kay Florian Schmitzberger schrieb: Dear All, Is there a way

[ccp4bb] XDS - resolution limit

Dear All, Is there a way to get XDS to include reflections in the far corners of diffraction images. XDS seems to take the high-resolution limit automatically from the edge of the images corresponding to the smallest radius from the center. In my case, with the keyword set to "INCLUDE_R

Re: [ccp4bb] refinement problem of labelled RNA complex

Hi, It's much easier to begin with the cif file created by Refmac5 itself, but this cif file needs to be checked and corrected manually for the restrains. Certainly, Iodine is not happy with the current restrains. Most of the time, i have found problems beginning with the protonation and th

Re: [ccp4bb] crashing-out protein eluted from Nickel column

Hi, In addition to the tips already suggested, you could also try to elute your protein with histidine.. I've got a protein that crashes out with imidazole as well, and I have succesfully used 200mM histidine for elution (using either KPi or MES buffer in my case). Cheers, Ronnie On Feb

[ccp4bb] refinement problem of labelled RNA complex

Dear all; I am a fresher of Refmac5. And now I'm trying to refine a protein and labelled RNA complex using Refmac. It's a Iodo-U labelled RNA. Unfortunately, these is no appropriate lib file in the current refmac dictionaries. So I use cif file which created by Refmc itself, surprisingly, the b

[ccp4bb] refinement problem of labelled RNA complex

Dear all; I am a fresher of Refmac5. And now I'm trying to refine a protein and labelled RNA complex using Refmac. It's a Iodo-U labelled RNA. Unfortunately, these is no appropriate lib file in the current refmac dictionaries. So I use cif file which created by Refmc itself, surprisingly, the b

[ccp4bb] pdbset surprise ?

dear colleagues, i just noticed a to me somewhat unexpected behaviour of pdbset. as it turns out, it seems to make a difference whether i do run pdbset all in one go, changing the cell and applying transformations at once: pdbset XYZIN ... << eof-pdbset cell spacegroup ... rotate euler shif