[ccp4bb] Saving Coordinates of an Unnatural Amino Acid in Jligand
Hi All, Apologies in advance for a potentially dumb question. I generated a cysteine adduct (DHZ) in JLigand. I can save the .cif and link file and I can get it to refine in Refmac just fine. For a different purpose, I need to save the coordinates of this unnatural amino acid, but when I go to Save Coordinates > it won't let me seem to do it. If I unlink my CYS and my molecule then I can Save Coordinates > CYS or LIG just fine. Thanks in advance for any help.
Re: [ccp4bb] Mg2+ or water
Hi, I'm not sure if it has been mentioned yet, but you could take an experimental approach if you still have crystals. You could soak them with EDTA/EGTA and if the density disappears that is good evidence it was Mg (or other divalent cation), if not then putatively water. You could also soak with Mn (assuming the Mn will bind the Mg site) and look for anomolous signal. John
[ccp4bb] Refmac remove restraints on targeted atoms
Hi, I would like to use Refmac (via ccp4i) to do normal restrained and TLS refinement. But, I would like all restraints to be removed from one ligand and one water only (everything else restrained as usual). How can I do this? I have what I think is a reaction intermediate that I want to be placed where it should by density alone, ignoring clashing. Thanks, John
[ccp4bb] .phs file conversion
Hi, I have a .phs file with map coefficients that I would like to open in pymol. So, I would like to convert the file to either a ccp4 or cns map file, or a file format that pymol will recognize. I do not have an .mtz file with the same map coefficients included. Can anyone help me? Thanks, John
[ccp4bb] unstable refinement
Hi, I would like to survey the group for causes and potential solutions to unstable refinement (the steady and upward drift of R and Rfree in each cycle of refinement). I am currently aware of the following potential causes: twinning (meohedral, pseduomerohedral, or epitaxial), anisotropy, pseudosymmetry, the lack of appropriately tight geometric constraints, and extraordinarily high b-factors. If anyone has run into any other causes of unstable refinement, I would like to hear about them. Thanks, John Bruning
[ccp4bb] easy way to make alternate conformers?
Hi, I am looking to take a pdb and make several altertnate conformers of the whole protein molecule. Is there an easy way to do this? Thanks, John Bruning
[ccp4bb] phenix mtz to ccp4 mtz conversion
Hi, I have an mtz file from Phenix I am trying to convert for use in Refmac. The labels are currently: H K L I-obs SIGI-obs R-free-flags I can't seem to get it to work. I am using Import, it runs, spits out a new mtz, and then Refmac complains about the labels. What is the easiest way (ie what program in ccp4 and usig what parameters). Thanks, John Bruning
[ccp4bb] Suse 10.2 install problem
Hi, I installed ccp4 (along with others such as coot) on Suse 10.2. Everything seemed to go well at first. The gui pops up normally. But when I try to run a process the gui shows the process as "starting" and it hangs there never switching to "running". And there is no log file available in the gui as well. Any ideas? Thanks, John Bruning
[ccp4bb] SAD question
Hi, I have some questions regarding SAD. Can one use Scaleit to initially analyze anomolous data when doing SAD (ie to get the scaleit.summary statistics)? How does one properly prepare the flags and mtz file for SAD (ie what program to convert the sca file to mtz and properly; I am coming from scalepack where I used the anomalous button clicked on)? Thanks
[ccp4bb] luzzati numbers in ccp4/refmac
Where can I generate the following numbers in CCP4 coming with pdb and mtz from Refmac? Luzzati SigmaA (obs) Luzzati ESD (R-free set) Luzzati SigmaA (R-free set). If the answer is sfcheck, where exactly are the numbers located, all I can find is Luzzati ESD overall?
[ccp4bb] R-free error in highest resolution bin
When using Refmac how does one find/calculate R-free error in the highest resolution bin?