Sorry, I was wrong about using STDEV in Excel. Instead you would need to put
in a formula to calculate the root mean square of your distances. On
Tuesday, 17 September 2019, 15:14:02 BST, Jonathan Cooper
wrote:
I think LSQKAB can output a list of CA distances of two structures. Might
Yet another way is:
phenix.superpose_pdbs fixed.pdb moving.pdb selection_fixed="chain A and and
resseq 1:10 and name CA" selection_moving="chain B and resseq 1:10 and name
CA"
or using the GUI.
Pavel
On Tue, Sep 17, 2019 at 8:06 AM Folmer Fredslund wrote:
> Dear Kyle,
>
> As other non-CCP4 sol
Yes I think I got it, along with invitations to speak at conferences on opening
up the North Shipping route or a bit closer to home, nanotechnology. Most of
these go almost automatic in the trash as they are just that, there is quite a
big market out there for predatory conferences, see also
ht
*Curate, validate, and standardize macromolecular structures from the
PDB community. Participate in exciting projects with significant impact
on the scientific community.*
Data archives are critical to research and education. They provide safe
and secure storage of valuable scientific data, an
I don't know if anyone else got this mailing. The conference
is being run by an organization called Allied Academies. It
was interesting to look up Allied Academies in wkipedia.
Frances
=
Bernstein +
HJF is seeking a Postdoctoral Fellow to support the Infectious Disease program
of Dr. Marzena Pazgier
(https://www.usuhs.edu/national/faculty/marzena-pazgier-phd) of the Department
of Medicine of Uniformed Services University of the Health Science (USU) in
Bethesda, MD.
We are looking for a hi
Well LSQKAB is set up to do this.
You ask (not sure of the key words - always use gui or coot..)
FIT CA 7 15 chain A
match CA 21 29 CHAIN B
then you can add more spans as required ..
You can do it in COOT
Calculate
LSQKAB - then select which residues to fit
or from GUI1
However both LSQKAB LS
Hi,
Thanks everyone for the answers!
I was able to identify my R free sets and they are the same =D
Best regards
Mariana
De: CCP4 bulletin board em nome de Eleanor Dodson
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Enviado: terça-feira, 17 de setembro de 2
On 09/16/2019 06:29 PM, Mariana Ajalla wrote:
Dear all,
We tried to use the Rfree set from a lower resolution data with a higher
resolution from the same Crystal. To do so We used aimless at ccp4i with the
option use free flag from another mtz file and extend the data.
I think it worked, but
If you use either GUI2 or GUI you simply name the old file you want to take
the FreeR flags from..
The pipeline then initiates the steps catalogued by Robbie..
Eleanor
As Tim, and others say, you can assign new FreeR flags, but dont get upset
when starting refinement with the prevuis model you se
This is probably a good opportunity to say that the USF has moved to
https://github.com/martynwinn/Uppsala-Software-Factory
Gerard asked for this so that they wouldn't be lost. I haven't put any effort
into checking the binaries or compilation, but I will do what I can on a best
effort basis ..
Dear Kyle,
As other non-CCP4 solutions have also been suggested, perhaps I can suggest
using PyMOL?
https://pymolwiki.org/index.php/Align
Here's a nice wiki article about what you can do with the align command.
If you're already familiar with scripting languages it's quite easy, and
you can load
Hi,
(good old) LSQMAN from the Uppsala Software Facotry will do this for you. First
you align the structures based on the subset of atoms you want to match, then
use the RMSD command to calculate the rmsd for the subset of atoms you are
interested in.
Best wishes,
Massimo
--
Dr. Massimo Degan
I think LSQKAB can output a list of CA distances of two structures. Might be
easier to fit them first in Coot since LSQKAB can be a pig to run and you may
have to use the command line. You could then select the region(s) you are
interested in and use a spreadsheet or a script to calculate the RM
Hello,
I admit that I only found the solution to import the pdb's after
alignment of the body of the protein into a spreadsheet (LibreOffice
Calc) and then to calculate the rms of the atoms of the loop (or of
the CA atoms of the loop).
Best wishes
Wim
On
Hi all,
What is the best/easiest way to calculate RMSD of a loop for 2 c-alpha aligned
structures?
Thought I could do this in Coot but I only see this if I align the specific
loops, which I don't want to do.
Thanks,
Kyle
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