[ccp4bb] [Off-topic]: Looking for a used R-Axis IV++ detector (USA)
Dear all: If anyone is willing to give away an R-Axis IV++ detector (for free or for a reasonable price) that we could use as is or dissect for parts (especially the laser assembly) please contact Frank Whitby (fra...@biochem.utah.edumailto:fra...@biochem.utah.edu). We are willing to travel (USA) or arrange packaging and shipment. Your help is much appreciated. Thanks, Vish
Re: [ccp4bb] help on preparing EM map for mask generation and molecular replacement
Hi Fei: I once had the same error message when using an EM map as an MR model. To make this work, you need to change your map's axis order from XYZ to whatever is appropriate (in my case it was ZXY) and also change the spacegroup to P1 using the CCP4 program maputils. In the CCP4i GUI, you do as follows: 1) Go to maputils: Map and Mask Utilities - Edit/Rotate Maps Masks. 2) Choose Edit a map/mask file for a map file. 3) Choose your map as input and choose an appropriate output file name. 4) Under the Edit file section, enter Space group as 1 and Change axis order to ZXY. You can get this from mapman's header when you load the map or CCP4 log file header from the failed SFall run. Alternatively, you could try all possibilities in the drop-down list. SFall should run fine using the output map from maputils. Best, Vish -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Fei Li Sent: Sunday, November 10, 2013 4:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] help on preparing EM map for mask generation and molecular replacement Dear experts, I'm planning to use a EM map to generate a mask for density modification and also potentially use it in molecular replacement. But I'm stuck on how to make this EM map to behave now. The original EM map was a reconstruction from 2D helical tube. The file was huge (containing several layer of the protein) and ended with .map. Our computation collaborator had already cut out a dimer, which is what I'm interested in, and put it into a small unit cell just slightly bigger than the dimer density. this file is ended with .mrc. I can open both file with coot and chimera fine. I tried to convert the dimer map into a .mtz file but when I try to use any of the ccp4 program (sfall, mapman etc), I always get error message on something like map and mask grid samplings do not match, Fatal disagreement between input info and map header or Incorrect sampling grid factors 40 29 45. I'm thinking it may be the unit cell that it is already in. But as I'm not familiar with Chimera, I couldn't figure out how to remove it. Also, how to choose and/or specify a proper grid? Any suggestion on how to make this EM map to work is high appreciated. Thank you very much! Best regards, Fei Fei LI Graduate Assistant 310 Biochemistry Building Department of Biochemistry and Molecular Biology Michigan State University East Lansing, MI 48824
[ccp4bb] Off-topic: Carboxypeptidase
Hi All: I wish to identify and remove unstructured regions at the C-terminus of my protein for crystallization and am considering using carboxypeptidase digestions to achieve this. 1) I would like a protocol and your preferred source of commercial carboxypeptidases as well their storage conditions. 2) Do I need to use a mixture of different carboxypeptidases? If so, which ones? 3) Is ESI-MS intact mass analysis a good way to identify the post-treatment C-terminus or does this treatment typically yield a large mixture of C-termini? 4) Any published references to this approach would be appreciated. Thank you. Best, Vish
Re: [ccp4bb] Off-topic: Fungal growth in robot trays
Dear All: Thank you for your responses. Here is a summary of suggested fixes: 1. Cleaning the supply carboy and lines with bleach and flushing thoroughly with DD water afterwards 2. Adding 0.02% sodium azide to the protein 3. Adding 0.02% azide to commercial screens 4. Adding 0.02% azide to the water used for washing 5. Using fresh screens and storing them at low temperatures (4 or 12 degree C) 6. Manually dispensing the reservoir solution using a multi-channel pipette 7. Using a Mosquito robot (it uses fresh needles each time) Best, Vish From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Viswanathan Chandrasekaran Sent: Friday, March 08, 2013 4:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Off-topic: Fungal growth in robot trays Dear All: I would like some advice on getting rid of persistent fungal growth in 96-well sitting drop crystal plates that were set up using a Phoenix robot. 24-well sitting drop trays prepared by hand don't have this problem. Washing the robot with 0.5% bleach followed by plenty of water had no effect. Is adding sodium azide directly to commercial screen hotels (or the protein sample) a good idea? If so, how much should I add? Other suggestions are welcome. I will post a summary of all replies. Thank you. Best, Vish
