Hi,
I copied the file Paul recommended into
lib/python2.7/site-packages/coot and I'm now able to download
coordinates and maps from EBI from within 0.9.8.1 again. Thanks.
This file doesn't work in 1.0.01 because that program uses python 3.8.
Dale Tronrud
On 6/8/2023 3:55 AM, Paul
skills are limited.
What do I do to download PDB's and maps again?
Dale Tronrud
To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
This message was issu
Zinc at 10% occupancy.
Sure, look at your map with a low contour level -- Just be aware
that you are looking at a low contoured map.
Dale Tronrud
On 5/3/2022 6:32 AM, Paul Emsley wrote:
On 02/05/2022 20:19, Dale Tronrud wrote:
When I watch people model building I see many scrolling the
con
out regard for the numeric
value of the level, apparently just choosing a value that makes the
peaks appear the way they prefer the peaks to appear. This way of
choosing a contour level seems dangerous to me as it seems to bias the
appearance of the map towards the modeler's expectation.
Dale Tronrud
O
tle large to just click around and hope to stumble
upon the place I want to look at.
Thanks for your help
Dale Tronrud
To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
an slowing the calculation.
Dale Tronrud
On 11/20/2019 11:36 AM, Daniel Larsson wrote:
> Hi Karim,
>
> If in doubt, you can load both maps and use the original one for
> refinement but hiding it and use the smooth map for visualization.
>
> Regards,
> Daniel
>
>
>
On 1/31/2017 11:51 AM, Paul Emsley wrote:
> On 31/01/17 17:54, Edwin Pozharski wrote:
>> Whatever the rationale was, there is a structure in the PDB that has
>> alternate conformer of a residue listed with different residue type -
>> A is arginine and B is glutamine. Coot fails to load the model
residue into the chain.
Dale Tronrud
On 1/31/2017 9:54 AM, Edwin Pozharski wrote:
> Whatever the rationale was, there is a structure in the PDB that has
> alternate conformer of a residue listed with different residue type - A
> is arginine and B is glutamine. Coot fails to load
atom I am, indeed, taken to 209D.
Dale Tronrud
-BEGIN PGP SIGNATURE-
Version: GnuPG v2.0.22 (MingW32)
iEYEARECAAYFAlSnI7QACgkQU5C0gGfAG11ZyQCfXUIo8Jh5t9NzlUEKb42E5yrR
liUAoJatGSTMU5tLZBp1DkTx7cUhgCKL
=qsBa
-END PGP SIGNATURE-
and mask out certain
features, that's a different kettle of fish.
Dale Tronrud
On 5/29/2014 2:20 PM, George Devaniranjan wrote:
Hi,
This is really 2 questions, one related to the other coming from
someone who is just starting to learn/use CCP4/COOT so this
question might sound rather naive
:
Essentially I want to use COOT's Calculate--map sharpening
but only use the backbone atoms in the process.
On Thu, May 29, 2014 at 6:08 PM, Dale Tronrud
de...@daletronrud.com mailto:de...@daletronrud.com wrote:
Hi,
Your question is vague so I will try to guess what you want
with the integrated Intel graphics.
Is the 5000 version of their graphics good enough for Coot to work
nice? I am not interested in stereo.
Dale Tronrud
-BEGIN PGP SIGNATURE-
Version: GnuPG v2.0.22 (MingW32)
Comment: Using GnuPG with Thunderbird - http://www.enigmail.net
I was looking for the download site for Coot but the links have
have found point to
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
but there is nothing there. Where do I go to find prebuilt coot
binaries?
Dale Tronrud
Very nice wiki but it points back to the same, empty,
directories.
Dale
On 09/03/2013 01:08 PM, Bosch, Juergen wrote:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installing_Coot_on_Linux
Jürgen
On Sep 3, 2013, at 4:04 PM, Dale Tronrud wrote:
I was looking
We seem to be having a communications problem. I have looked
in http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/,
there is nothing there under release. pre-release has a few
files but not a variety of distributions. This location appears
to be broken.
Dale Tronrud
On 09/03
phytol tails are the same you can compare any chlorophyll-like
molecule to the tails in this model to see if you are correct.
Dale Tronrud
bph-med-res-v030.cif
Description: CIF chemical test
and then we can discuss the fact that contouring in
rmsds is not the right thing to do. Appropriating the word sigma
merely gives the illusion that some sort of statistics is being done.
Dale Tronrud
Cheers
-- Ian
Cheers
-- Ian
a little reassurance.
Dale Tronrud
suppose that the output of Coot
and mapmask would help there, although for clarity you would have to explain
how sigma is derived (it is often opaque, it seems to me).
Paul.
On 22/12/10 23:37, Dale Tronrud wrote:
The 12 sigma I want to put in the paper is from the Fo-Fc map
where the rms is more
It would be helpful if you said exactly what kind of CIF you
have. The CIFs from the PDB-RCSB only contain observed structure
factors or intensities. If you want a map you have to go to the
Electron Density Server.
Dale Tronrud
subh wrote:
Hi,
I am trying to open the .cif file (in coot
at a
time the result will differ depending on the end of the side chain
they start deleting atoms from. I don't know if this is a serious
problem, or even a problem at all.
Dale Tronrud
2) Should a few folks align themselves with my opinion, can COOT's
behavior be modified without unintended
but have not found a definition.
Your help will be appreciated.
Dale Tronrud
22 matches
Mail list logo
