[ccp4bb] About sel-met oxidation

Hi all, I am now preparing to label my protein with selenium-methionine for phasing. As I have heard that selenium-methionine is prone to oxidation, so is it a must to add reducing agent all along the purification? if so, which reducing agent and what concentration is better ? and any alternati

Re: [ccp4bb] maprot question

Thank you Eleanor and Kevin, Eleanor suggested separating the two tasks. Eventually, I changed the cell with maprot and then used MAPMAN to zero the map below the cut-off level. Kevin described how maprot works and suggested down-scaling the map to have more reasonable values for densities. Thes

[ccp4bb] resolution shells for each bin in scala?

Hello ccp4'ers Where is / how can I obtain the resolution shell for each resolution bin in scala? My eyes can't seem to find it. Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys

Re: [ccp4bb] Twinning

> -Original Message- > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of > Rana Refaey > Sent: Monday, August 03, 2009 12:26 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Twinning > > Hi all, > I have a few datasets that I think are twinned for several reasons. > 1)

[ccp4bb] Twinning

Hi all, I have a few datasets that I think are twinned for several reasons. 1)The Rfree and Rmerge are both stuck very high. 2) The L-test for twinning in Scala shows twinning 3) Also the centric and acentric movements suggest twinning. 4) The spots do not match the predication from Mosflm (No

Re: [ccp4bb] Rfree going up

maybe those loops are right - ish. Eleanor kumar wrote: Dear members, I am refining a structure and I notice that when I delete loops that have none, or very little density, the Rfree (which is around 40% at 3.4A) goes up instead of going down. Much of the remainder of the molecule is in good d

Re: [ccp4bb] CCP4 / Ubuntu 9.04 64-bit

hi I installed CCP4 with Coot downloaded as a binary from the CCP4 website on a 64bit Ubuntu 9.04. The installation was flawless and the setup scripts ran like a charm. however, when i type ccp4i to get the GUI. i get the following error message: exec: 4: /usr/local/xtal/tcltk++/bin/bltwish:

Re: [ccp4bb] question of extra high B factor

Dont forget the confusing interaction between recorded B factors in a PDB file and TLS parameters. This Q is still I think unresolved but you need to be careful! Eleanor Edward A. Berry wrote: Interesting that the correlation between B-factor and resolution didn't show up in the QDB as recentl

Re: [ccp4bb] Phase matching program(s)

I cant answer for cphasematch but I believe it uses a resolution dependent phase analysis discussed by Woolfson and Lunin in the 1980s and similar to the method used to calculate the MAPCC used in SHELXE That checks for a possible origin shift as well as analysing difference - but I presume

Re: [ccp4bb] Density modification

Can you send the command script? Eleanor kumar wrote: Dear CCP4¹ers, I¹m trying to run DM for after Refmac on an MR solution but it crashes. I do have the FOM¹s listed in my log file. I get a similar error when I use the mtz file from Phaser¹s SAD + MR. I¹d appreciate any help. Thanks! Kumar A

Re: [ccp4bb] maprot question

I CANT BE SURE of what has happened BUT maprot is a very complicated procedure and your script is trying to do 2 things at once - change the cell and apply the mask. I would try changing the cell first, then generating the mask, then applying it or else: generate mask, apply mask, then change

Re: [ccp4bb] how to run detwin?

I guess someone has answered this? Q1 Before detwinning data you must process in the lower symmetry.. Comment. It may not bre necessary or sensible to use detwin - the resukltant estimates of I are pretty unreliable.. You can use twinned data usually to solve an MR problem, and the refine