[ccp4bb] Coot installing problem

2012-06-14 Thread Young-Jin Cho
Hi, I am using old RedHat now and am having some problem for using new version of coot. When I downloaded coot-0.6.2-binary-Linux-i386-rhel-5-python-gtk2.tar.gz, and simply untared and went to bin directory. When I typed as following it gave me following message: $ ./coot COOT_PREFIX is

[ccp4bb] Pointless (P41) vs. Phaser (P43)

2011-10-11 Thread Young-Jin Cho
Hi all, I recently got diffraction data of 214 AA protein. When I processed the data, pointless suggested me a space group as P41. However, when I ran Phaser with 'all choices of alternate space group', it gave me a pdb file with P43. Additionally, phenix.xtriage suggested me P422 with twin laws

[ccp4bb] Sodium ion vs. Water

2011-08-02 Thread Young-Jin Cho
Dear CCP4 experts, I would like to ask if there is a clear way to distinguish Na+ and HOH molecules in the electron density map. The table I have suggests Na to O distance lies between 2.35 and 2.45 that is very hard to discern the difference of these two candidates. Na+ may have several

Re: [ccp4bb] AMP-PNP Hydrolysis

2011-02-14 Thread Young-Jin Cho
Hi Steve, With my experience, it is (very) common to see AMPPNP is hydrolyzed to AMPPN (supposedly) with my protein. Although the literature often reported AMPPNP as a stable ATP mimic, such a luck wasn't true with my case, maybe same as you. If you go to Sigma website where I purchased, it may