Hello,
I'm a new user of Coot. I have a density that has the shape of a helix. I
sort of have an idea of what sequence should go in there, but I haven't
resolved the structure near it from both the C- and N-terminai sides.
How can I start placing amino acids in the density without having a
termin
I have a 6 chained structure of three tubulin molecules, 3 alpha and 3 beta
subunits.
How come sequence draw shows only three sequences and not the rest?
Regards.
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I have three structures open in Coot. I have only one displayed that I was
working on. Oddly enough, when I press undo, I get a warning about how Coot
can't undo modifications to a structure that's not displayed.
When I display all three structures, Coot will make undo's to the the other
ones but
Two questions:
1) I like to set my structure view to show only the alpha carbon backbone.
Is there a way to show the side chains of only selected residues?
2) I have a tyr and an arg that I think are interacting (sort of clashing).
How can I refine both residues together to converge on possible i
Hello,
I'm working with a lattice made of a tubulin monomer that I modeled and
refined in Coot.
I have fitted other units of the monomer along the length and to the side
of my monomer in a cryo-EM map to study tubulin interactions with non
tubulin proteins.
My problem: sometimes I have to refine
I want to copy the output matrices of SSM, how to display the console
window?
Regards.
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I have a large structure loaded in Coot. The middle mouse click is often
mistaken for a center around atom action whilst trying to navigate the map.
Is it possible to assign the center around atom function to another key
combination, like ctrl and middle mouse?
Regards.
#
Hello,
I want to write a script that does the following:
for a bunch of chains and atom numbers:
go to chain letter and atom number
do sphere refinement
if refinement parameters are ok:
accept
else:
go to chain letter atom number
if refinement parameters are ok:
accept
else:
continue
I have very
But that function should already be implemented in the green flags that I
get in the accept refinement dialog, no?
On Sun, May 19, 2019, 7:19 PM Paul Emsley wrote:
> On 19/05/2019 21:40, Ahmad Khalifa wrote:
> > Hello,
> >
> > I want to write a script that does the fol
pass
> else:
> apply_undo()
>
> You will still need to write the stats_are_acceptable function with your
> own cutoff values.
>
> Kind regards,
> Paul
>
> On Mon, 20 May 2019 at 02:30, Ahmad Khalifa
> wrote:
>
>> But that function should already b
I know I can either force beta strands or alpha helix restraints while
refining/regularizing, but what about 310 helices?!
Regards.
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Reinstalling didn't solve the problem:
https://youtu.be/jXZ5bZsuK3g
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Hi,
I want o display the entire biological assembly by generating all the NCS
copies from the BIOMT record in my pdb file.
Currently, I open the structure in chimera, generate the NCS copies I need,
save them and then open in coot, but is there a way to do that on the fly
in Coot?!
Regards.
###
How does Coot guess the direction of the chain? How confident is this
assignment?
Regards.
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Is there a limit to the number of chains that Coot can display in a
structure? A lot of the chains in my structure weren't loaded.
The missing chains appear to be random, but reopening the coordinate
file results in the same missing chains.
How can I fix it?
#
Merging 50 chains results in serial numbers that have characters in them.
After 9, it starts with A, A0001, A0002,etc.
I assume this is not Coot's fault, because some restrictions in the
serial number column size?! but I wonder if there's a work around this
to be able to deposit my st
This error is printed by the PDB deposition portal.
"File upload failed
Please review the errors below and try again.
Coordinate issues
ERROR: 'A' is not a number.
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM A N PHE j 389 308.681 214.654 329.22
I want to either color chains of the same structure differently, or turn on
environmental distances between molecules (which I can color differently).
If neither can be done, I think it's a feature worth adding in future Coot
releases.
Regards.
###
The Coot sequence view window assigns different colors to residues. What
does this coloring mean exactly?
Regards.
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Hi,
I followed this tutorial to add a NAG to my structure
http://legacy.ccp4.ac.uk/tutorials/tutorial_files/jligand/1_glycan.html.
My question is, how can I add another NAG to make a NAG chain?
Regards.
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Can I install Coot on ubuntu 18.04? I get this error here "error while
loading shared libraries: libpng12.so". As far as I read v12 of libpng is
no longer available in ubuntu 16+. If there's a work around this that
doesn't require admin permissions, please let me know.
Thanks.
###
When I apply an ncs residue range from a master chain, it gets propagated
to all slave chains, but I want the change to propagate to only a
particular chain, without having to undo all the changes in the other
chains!
Alternatively, I wonder if there's a way to build a segment from a template
that
Thank you so much. It did work for me.
Cheers.
On Tue, Dec 7, 2021 at 6:06 AM Bernhard Lohkamp
wrote:
>
> Hi Ahmad,
>
> > When I apply an ncs residue range from a master chain, it gets
> propagated to all
> > slave chains, but I want the change to propagate to only a particular
> chain,
> > wit
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