[ccp4bb] protein structure for high schoolers

Hi- I am trying to help my former chemistry teacher set up a demonstration of protein structure for her class. I'd like to include electron density maps, and maybe show an enzyme active site. Are there suggestions from the BB on the easiest way to do this? Would pymol be the program of choice, or

[ccp4bb] LABELIT with XDS

Dear all, I'm able to index my images in LABELIT. Is it possible to use that indexing solution in XDS? James

[ccp4bb] conversion of cyroEM reconstruction from MRC to CCP4 format

Hi all- I'm trying to convert a cryoEM map from FREALIGN for use with various CCP4 programs, or with MAPMAN. Even though the MRC format is derived from the CCP4 map file format, every program I've tried fails to open it, (except for Chimera which displays the map but cannot save it to another form

[ccp4bb] refmac, twinning, restraints

Dear all, Can any one comment on setting up restraints for refinement against merohedrally twinned data in Refmac? I find that refinement distorts the geometry (90% allowed in the Ram. plot becomes 60% after 10 cycles). Decreasing the weight term to 0.5 or 0.1 seems not to improve the ref

[ccp4bb] indexing choice for C2

Dear all, I believe I've run across a case similar to that described recently in Zwart et al., Acta Cryst. (2008) D64, 99-107: "Given the pseudosymmetric nature of the lattice (pseudo- rhombohedral), C2 can be embedded in the higher symmetry lattice in three different ways (see Fig. 4), co

Re: [ccp4bb] Scaling of intensities

Dear ccp4ers, I hope you won't mind revisiting more twinning questions, but this thread has me considering whether I have treated some recently collected, most likely twinned, data in the best way. Last week I was told that I ought to let phenix.refine choose freeR flags for twinned da

[ccp4bb] installing Phaser EP

Hi all- I'm trying to get Phaser EP working through ccp4i on an intel Mac. I've tried re-installing both ccp4 and phaser from the automatic downloads section of the website, but Phaser EP still does not appear in the program list. Can anyone suggest how to fix this? --James

[ccp4bb] stereo in coot with RHEL 5

Hi- There seems to be a problem enabling stereo with coot on RHEL 5, which results in the error: CATASTROPHIC ERROR:: in gl_extras no GtkGL widget! WARNING:: switch to hardware_stereo_mode failed I've found mention of this through a google search, but no solution. Has anyone encountered this and

[ccp4bb] SFALL grid

Hi: I am trying to generate structure factors from a mask/map that I made with NCSMASK. I get the following error message in SFALL: The program run with command: sfall HKLOUT "/tmp/whittle/109_5_7_1_mtz.tmp" MAPIN "/home/whittle/projects/109_5/CCP4/center_50.msk" has faile

[ccp4bb] coot and video card fan

using coot 0.3.1 from the redhat binaries. Would compiling from source perhaps fix the problem? Best, James Whittle