Dear all
A second postdoctoral position in the Integrated Structural Biology lab at The
International Center for Translational Eye Research (ICTER) in Warsaw, Poland,
is available for highly motivated biologists, biochemists, or structural
biologists, funded until the end of 2023. The position
Sorry to go back in time but distang is useful.
You set radii
Example:
distang xyzin CCP4_JOBS/job_100/100_adam_xyzout_coot_rebuild_1.pdb
RADI CA 1
end
will give all CA withion 2A of each other
distang xyzin CCP4_JOBS/job_100/100_adam_xyzout_coot_rebuild_1.pdb
end
Will give all C N O S
Hi Henrike,
I use CCP4's "contact" program:
#!/bin/bash
# find bad contacts: list all CA-CA distances < 3.8A between non-adjacent
residues
# in a well-folded protein, these should be very rare (1 contact in 1000
residues)
# KD 20.12.21
grep CA $1 > /tmp/temp.pdb
contact xyzin /tmp/temp.pdb <
Dear all,
We are looking into a way to find clashes / bumps between protein chains
(closer than van der Waals contacts).
Ideally, we would like to that with a script, for example, reading in a
pdb file, and giving back the number of clashes.
Of course, this is possible within Coot or PyMol,
Hi all,
We are pleased to announce that applications are now open (until 15 August) for
the CCPBioSim Training Week. The training will take place 19-23 September 2022
as a hybrid event in Leeds (UK) and online. The target audience is Masters and
PhD students, but everyone is welcome to apply
Dear all,
I am trying to reconstitute a 5' to 3' exonuclease bound to substrate RNA for
structural studies. For this, I would like to synthesize a 40nt ssRNA
containing a modified residue will inhibit the exonuclease activity eg: at
position 20. I could find from the literature that using
On 13/07/2022 19:18, Ravikumar wrote:
I would like to calculate One-dimension electron density profiles of
the different number of ions bound to an ion channel. Are there any
programs in CCP4/ Phenix which can do the same job as the MAPMAN
(UPPSALA electron density server) program to
Hi,
It’s not clear why you don’t use MAPMAN if that does what you want. If
availability is the problem, it is still here
https://github.com/martynwinn/Uppsala-Software-Factory
If you are prepared to do some Python, then 2 other options:
https://mrcfile.readthedocs.io/en/latest/readme.html
