Personally, I like the ability to at least have a sanity check of the
HETNAM with the dictionary - and if they do not match - do not use
it... Assuming people provide a unique name in their dictionary - even
if it is FOO1, FOO2, etc - this could catch the issue. This assumes
that the refinement
On 26/01/12 21:48, Ezra Peisach wrote:
Personally, I like the ability to at least have a sanity check of the
HETNAM with the dictionary - and if they do not match - do not use
it... Assuming people provide a unique name in their dictionary - even
if it is FOO1, FOO2, etc - this could catch the
All:
Although I also like Dale's idea of paying attention to HETNAM records, I think
we should stay in concordance with PDB rules and use HETNAM records only for
IUPAC names. Fortunately, the PDB also has HETSYN records and that is where we
place the BMS name (number) of a compound when we
Software
[mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Kendall Nettles
Sent: Tuesday, January 24, 2012 3:26 PM
To: COOT@JISCMAIL.AC.UK
Subject: Re: [COOT] New restraints, same name
That didn't come out right. What I meant to say was that he are often
comparing structures from a series of closely
On 25/01/12 16:46, Kendall Nettles wrote:
I know my message was not very clear. I'm thinking of occasions where the
ligands are symmetrical, or we have a mixture of compounds and are not sure
which regioisomer to fit. We would load the maps and models of other structures
with related
On 24 January 2012 17:53, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote:
Now that Coot uses the restraints dictionary to render ligands it has become
apparent that the method of doing so is problematic for typical working
situations.
Say for example your read in
complex-XYZ00123456.pdb in
Now that Coot uses the restraints dictionary to render ligands it has
become apparent that the method of doing so is problematic for typical
working situations.
Say for example your read in
complex-XYZ00123456.pdb in which the ligand is called LIG
You read in the dictionary for XYZ00123456 and
On Tuesday, January 24, 2012 09:53:55 am Paul Emsley wrote:
Now that Coot uses the restraints dictionary to render ligands it has
become apparent that the method of doing so is problematic for typical
working situations.
Say for example your read in
complex-XYZ00123456.pdb in which the
El 24/01/12 18:53, Paul Emsley escribió:
Now that Coot uses the restraints dictionary to render ligands it has
become apparent that the method of doing so is problematic for typical
working situations.
Say for example your read in
complex-XYZ00123456.pdb in which the ligand is called LIG
On Tue, Jan 24, 2012 at 11:59 AM, Miguel Ortiz Lombardia
miguel.ortiz-lombar...@afmb.univ-mrs.fr wrote:
And really, is it so hard to give a unique identifier to each ligand?
I'm pretty sure it really is difficult (or at least inconvenient) for
the people at drug companies, because I've heard a
El 24/01/12 21:05, Nat Echols escribió:
On Tue, Jan 24, 2012 at 11:59 AM, Miguel Ortiz Lombardia
miguel.ortiz-lombar...@afmb.univ-mrs.fr wrote:
And really, is it so hard to give a unique identifier to each ligand?
I'm pretty sure it really is difficult (or at least inconvenient) for
the
That didn't come out right. What I meant to say was that he are often comparing
structures from a series of closely related compounds.
Kendall
On Jan 24, 2012, at 3:19 PM, Kendall Nettles knett...@scripps.edu wrote:
Renaming ligands is a nightmare if you have a lot of structures or
On Tue, 2012-01-24 at 15:26 -0500, Kendall Nettles wrote:
That didn't come out right. What I meant to say was that he are often
comparing structures from a series of closely related compounds.
But isn't it true that non-identical compounds should have different
names? Paul also refers to
As far as I understand complication arises from complexity of model building
programs. You may have many coordinate sets (not necessarily with same space
group or even related ones, you may have many electron maps, they may be
related to one or many coordinate sets). Ligand name that is valid
All:
At BMS, we use the same ligand identifier, e.g. LG1, for all compounds that
bind at overlapping sites. If we have multiple compounds bound in a single
structure, i.e. non-overlapping sites, then we would use LG2, etc. for them.
Using a common naming system makes it easy for upstream and
Hi All
As I see the best available solution is to go for coordinates all in one. I.e.
ligands description and the rest of structure in one file. It should be
possible to do it with mmcif.
then each ligand (apart from standard ones) will be property of a coordinate
set and no conflict between
I would like to second to most of Steven's, Seth's and Garib's points
and would welcome a change that would enable us to use the same three
letter code for different ligands within one coot session.
Renaming ligands in pdb and cif files is a good workaround, however it
is not more than a
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