[ccp4bb] Saving Coordinates of an Unnatural Amino Acid in Jligand

[John Bruning]

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

[John Bruning]

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

[John Bruning]

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

[John Bruning]

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

[John Bruning]

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?

[John Bruning]

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

[John Bruning]

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

[John Bruning]

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] luzzati numbers in ccp4/refmac

[John Bruning]

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

[John Bruning]

When using Refmac how does one find/calculate R-free error in the highest 
resolution bin?