I noticed the same problem with more recent versions of CCP4 (up to and
including 6.5.001) but failed to report it….
It seems that the problem occurs regardless of the atoms chosen for selection -
main, side or all - and with both v2 and v3 PDB files.
The 'LSQ Superpose’ in Coot can
Hi Almudena,
some graphic programs connect atoms based on distance only (draw a line
between two atoms that represents the covalent bond). I suspect this is
what PyMol does. Some may employ more information such as one encoded in
Monomer Library CIF files. Some try to do both. I suspect this is
On 04/02/15 17:21, Robert Byrne wrote:
The 'LSQ Superpose’ in Coot can superpose nucleic acids, but it is seemingly
not possible to define non-contiguous selections.
Admittedly there's no clicky-clicky interface, but you can do it and
it's described in the manual.
Dear all,
does anyone know why if I open a pdb in pymol (that appears normal and
fully connected in coot) it appears as if it was broken into pieces?
Thanks,
Almudena.
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical
Try adding b-ME/DTT/TCEP in your crystallization conditions, if its not
there already in your protein buffer.
On Mon, Jan 13, 2014 at 2:02 PM, Debasish Chattopadhyay debas...@uab.edu
wrote:
We crystallized a protein at 4 and 22 deg C in different conditions:
from ammonium sulfate in
I'm (still) using ccp4.6.1.1.
Scripts that used to superimpose one tRNA on another now all return the error
YOU HAVE FAILED TO FIND ANY ATOMS TO FIT
I've looked high and low for a reason for this and failed. The pdb files
themselves look normal and behave well in PYMOL. They have CRYST1
Dear Charlie,
could it be related to that furanose atoms now have primes (') instead
of asterisks (*) in their names?
Best,
Tim
On 02/04/2015 05:30 PM, Carter, Charlie wrote:
I'm (still) using ccp4.6.1.1.
Scripts that used to superimpose one tRNA on another now all return the error
YOU
Hi
This problem is almost certainly* because there is an orphan
ipmosflm.exe still running (this can happen when you get a Tcl error
and iMosflm stops unexpectedly {some people might call this a
crash}). At the moment you do have to kill the orphaned
ipmosflm.exe process from the
Tim
Well if you google for proton scattering by x-rays, the most relevant thing you
find are these emails!
d=0.26A would be well within the limit for a silver source.
Most charge density studies seem to be around d=0.5A - 0.7A, including the
crambin studies.
Dear Jacob,
Thanks for reporting this problem. Can you tell me what version of CCP4
you are using?
As an alternative, you can use MrBUMP via the CCP4-online service which
is available from here:
www.ccp4.ac.uk/ccp4online
It's still in development and only goes as far as the Refmac step
Hi Sacha,
I was imprecise. With unplaced I meant neither rotated nor translated.
Once you become post-rotationally SF based, you can in fact compute a F(env)
whole inclusion should improve the TF score.
What is not evident to me is how to use a mask and compute the Fs if the
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