Re: [ccp4bb] Question about merging of data from different crystals

Hi Yuan Cheng, You have received plenty of advice as to how to proceed with your problem. There is still one thing that no one mentioned, and in my opinion, is the simplest way to go about what you want to do. There are plenty of monoclinic cells with a beta that is very close to 90, but when

Re: [ccp4bb] Changes in Cell Constants

Hi Jacob That doesn't surprise me at all, though the example you heard is probably towards the extreme end of what we've seen. We have seen individual cell parameter changes up to 10% on soaking/freezing which could easily add up to 20-30% change in cell volume. One problem with freezing is

[ccp4bb] Converting map to mtz file

Dear All, I have masked a map in coot and exported it. Now I'm trying to use SFall to convert the map file to mtz file but I get the error msg: FATAL DISAGREEMENT BETWEEN INPUT INFO AND MAP HEADER. How to solve this? Any suggestion? Thanks in advance. Regards, Anita

Re: [ccp4bb] Sigma Cutoff in HKL2000 Data Processing

I guess you mean higher redundancy/completeness in the HIGHER resolution shells. Rather than decreasing that sigma cutoff, a better solution is to increase the profile fitting radius. The default value is fine for most lab-based detectors, but too small for most (larger) synchrotron detectors.

[ccp4bb] Beam time is available at the NSLS

Please visit the website at www.px.nsls.bnl.gov and select Get Access to Beam Time. The PXRR (Macromolecular Crystallography Research Resource at the NSLS) operates five beamlines for macromolecular crystallography (MX). Two of these beamlines are undulators: X29 is the most efficient MX

[ccp4bb] Alterate conformers destroyed by Refmac!

All - we're having a problem with Refmac (version 5.5.0102) in CCP4 6.1.2 that I compiled from source using ifort v11.0 on Centos 4.6. When I refine a structure with a HIS in alternate conformations (all atoms except N, C O doubled up) it completely destroys the sidechains of both copies. Same

Re: [ccp4bb] Alterate conformers destroyed by Refmac!

Few people had complains about this. It seems to be related with compilation. If you take the version from York's website then it should work fine. www.ysbl.york.ac.uk/refmac/latest_refmac.html I have compiled it for mac 10.5 and it does not seem to work on mac 10.4. I am trying to make

Re: [ccp4bb] Converting map to mtz file

Inverting a map with sfall has different restrictions on allowable gridpoints and axis order within the electron density map (due to FFT vs slow FT). Check what the sfall documentation lists as requirements for your spacegroup, and adjust the coot map output settings as needed (or if it's

[ccp4bb] polygon stand alone - updated version

Hello, An updated stand-alone version of the program POLYGON (Urzhumtseva et al., 2009, Acta Cryst, D65, 297-300) is available at http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Polygon/Polygon.html A number of bugs were fixed; in particular this version was successfully tested at a Mac

Re: [ccp4bb] polygon stand alone - updated version

Alexandre Urzhumtsev wrote: Hello, An updated stand-alone version of the program POLYGON (Urzhumtseva et al., 2009, Acta Cryst, D65, 297-300) is available at http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Polygon/Polygon.html A number of bugs were fixed; in particular this version was

Re: [ccp4bb] Alterate conformers destroyed by Refmac!

Not exactly the same setup, but maybe close enough. I used Intel's 11.1 compilers on RHEL4.8 to build refmac (5.5.0102 and 5.5.0105) and it will not run the refmac_tls script in the CCP4 example area. It turns out that the LAPACK libraries (3.0) that comes with RHEL4 and the Intel (11.1)

[ccp4bb] Using own orientation matrix with imosflm.

Hi All I have a predetermined matrix from labelit, how can I use it with imosflm? I add the matrix file under 'Images', but I cannot integrate. Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver

[ccp4bb] Postdoctoral position, MacCHESS, Ithaca NY

MacCHESS (Macromolecular diffraction at Cornell High Energy Synchrotron Source) has an opening for a post-doctoral associate to work on developing novel methods of 3D visualization of protein crystals mounted on a synchrotron beamline, for the purpose of crystal centering and motion planning

[ccp4bb] pdb submission with SS bond + alternate and author defined ss

Hello, I have two short questions about submitting a structure to the PDB: 1- How should I submit a structure that has a SS-bond with alternate free cysteines (knowing that the SSBOND record does not support alternate conformation)? 2- How can I keep my author-defined secondary structures

Re: [ccp4bb] measure detergent concentration

Only easy if you happen to have silica gel TLC plates and a chromatography jar lying around, perhaps from some phospholipid analysis: A strategy for identification and quantification of detergents frequently used in the purification of membrane proteins Laura R. Eriks, June A. Mayor, and Ronald

Re: [ccp4bb] measure detergent concentration

Weikai, We did it using NMR but you asked for a simple way so I guess I'm out of topic. Anyway, since I believe it is the most accurate method, here it is: using a high detergent concentration stock solution you can assign resonance peaks to your detergent molecule bonds. Then you can set up

Re: [ccp4bb] measure detergent concentration

Also depending on the detergent , If you have a detergent like decyl-maltopyranoside ( DM) or any other glycoside based detergent you can use the reaction with sulfuric acid  and phenol followed by Absorption  measurement to quantitate as detailed in Anal Biochem. 2005 Jan 1;336(1):117-24. A