On 22/02/2024 01:06, Kim, Sun Kyung wrote:
Hi Paul,
Thank you for your response!
I opened Coot from my terminal, and not seeing any diagnostic
information, but it just opens up coot.
There seems to be some confusion because I read this and think "that
cannot be." Are you reading what is
Hi Paul,
Thank you for your response!
I opened Coot from my terminal, and not seeing any diagnostic information, but
it just opens up coot.
When you mention I could try setting COOT_MONOMER_LIB_DIR or
REFMAC_MONOMER_LIB_DIR to the directory that containers the monomers… I’m not
sure as to
On 21/02/2024 02:50, Kim, Sun Kyung wrote:
Thank you Paul for that information. I will look into Acedrg and Grade2!
Sounds good.
I have an unrelated question… I’ve never encountered this before, but
all of a sudden my COOT is complaining that it doesn’t have restraints
for refinement…
Thank you Paul, for your reply! I was not able to locate the exact dictionary
but I think I was searching probably in the right folder… what is the file type
I should be looking for?
More pressing questions for me are about REDUCE that’s used in COOT:
1. In COOT, does REDUCE take into
Hello Kate,
Attached is an example conn file: it is in a folder called
coot-molprobity and has the required format for input to Reduce.
> In COOT, does REDUCE take into account pH and local changes in pKa of
atoms when determining protonation states?
In SMILES-speak: NCC(=O)[OH] and
It is in the directory from which you started coot (that is, if coot can
create and write to such a directory (if not it is in your home directory)).
Paul.
On 15/02/2024 23:51, Kim, Sun Kyung wrote:
Thank you Lucrezia for your informative reply!
You suggested I look into coot-molprobity
Thank you Lucrezia for your informative reply!
You suggested I look into coot-molprobity output directory. Where can I locate
this directory?
Thank you.
Best,
‘Kate’ Sun Kyung Kim
From: Lucrezia Catapano
Date: Friday, February 2, 2024 at 6:21 AM
To: Kim, Sun Kyung , COOT@JISCMAIL.AC.UK
Dear Kate,
Just to clear up some potential confusion and contradiction between Lucrezia's
and my answer. Coot has various ways in generating hydrogens, internally using
the dictionaries as Lucrezia nicely mentioned and explained, and externally
using e.g. refmac or reduce (as I mentioned
Dear Kate,
Coot adds hydrogen atoms according to the dictionary. If you want to change the
protonation of a ligand, you'd do that by modifying the actual monomer
dictionary. We typically use Acedrg to generate dictionaries.
For example, in the case of a ASP residue, the modification which
> Hello,
>
>
>
> I’m using the Coot 0.9.8.91 EL. I am working jointly with a computational
> team who are doing simulations on our PDB model. I’ve added hydrogens to
> my model using Coot’s Validate -> Probe clashes function. The computational
> team asks, when COOT adds protons using the probe
Hello,
I’m using the Coot 0.9.8.91 EL. I am working jointly with a computational team
who are doing simulations on our PDB model. I’ve added hydrogens to my model
using Coot’s Validate -> Probe clashes function. The computational team asks,
when COOT adds protons using the probe clashes
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