Is it safe to assume that the section headers in mol2 files are all
@TRIPOSsomething
or is all that's guaranteed the initial @?
http://tripos.com/data/support/mol2.pdf has everything TRIPOS, but that's
defining the 'Tripos Mol2 File Format' and I don't know if someone else has
defined a
On 20 Mar 2012, at 12:34, Eleanor Dodson wrote:
I would like to use this to check an existing ligand. I have the PDB refined
according to a cif file, and that cif file used for input to REFMAC and
phenix.
I dont want to lose the atom names assigned there so is it possible to start
GRADE
On 2 Mar 2012, at 16:02, Regina Kettering wrote:
Rajesh;
I am not sure that you have a high enough data:refinement parameters ratio to
refine TLS. It just adds more parameters to refine that can lead to
over-refinement of your model, especially at the 3.3 A.
TLS only adds twenty
On 11 Jan 2012, at 02:13, Artem Evdokimov wrote:
There are two sides to this qustion: the scientific one is actually easier to
answer in generic terms - but I also would like to point out the very recent
example of a mystery that required very high resoluton (and orthogonal
techniques) to
On 11 Jan 2012, at 11:36, Thomas Womack wrote:
On 11 Jan 2012, at 02:13, Artem Evdokimov wrote:
There are two sides to this qustion: the scientific one is actually easier
to answer in generic terms - but I also would like to point out the very
recent example of a mystery that required
The patch in
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;325e1870.1112 solves the
problem with 3u57.
A few days ago I read the interesting paper
http://journals.iucr.org/d/issues/2011/01/00/dz5216/dz5216bdy.html referring to
a crystal structure containing a diselenide bond; I
which is a binary file; presumably that's produced with some
kind of compiler from some kind of source file, but I'm not sure how to start
looking for the compiler and the source.
Yours sincerely,
Thomas Womack (Global Phasing)
On 11 Aug 2011, at 17:40, Diana Tomchick wrote:
A quick glance at the header of the PDB file shows that there is one glaring
discrepancy between it and the table in the paper that hasn't been mentioned
yet in this forum. The data completeness (for data collection) reported in
the paper is
On 8 Jul 2011, at 19:13, Katherine Sippel wrote:
I know that the PDB updated its validation server in May as described in
their news link but it seemed to indicate an increase in output options
rather than a change in criteria. Is anyone aware of what changes were made
to the validation
On 16 Jun 2011, at 17:19, Pavel Afonine wrote:
Hi,
On Thu, Jun 16, 2011 at 7:49 AM, Jan Dohnalek dohnalek...@gmail.com wrote:
Modeling more UNKNOWN atoms might be the future for these cases?
one needs to specify chemical element type in 77-78 position, otherwise these
records are
,
Thomas Womack (Global Phasing)
On 4 Oct 2010, at 11:15, Leiman Petr wrote:
Dear all,
Coot behaves in a very strange way on my student's MacBook (32bit) running
MacOS X 10.6.4. Both versions of coot are affected - the precompiled Prof.
Scott's one and the compiled from source.
It cannot read in MTZ files (quote: This
On 15 Sep 2010, at 18:04, Ed Pozharski wrote:
On Wed, 2010-09-15 at 07:57 -0700, Pavel Afonine wrote:
if you refined your structure with H, then you should deposit it with
H
sure. But the structure is not *refined with hydrogens* when they are
in predicted positions. Following the same
On 27 Aug 2010, at 10:55, Petr Kolenko wrote:
Dear crystallographers,
I have a structure at 3.3A resolution, 16 identical chains in AU, merohedral
twinning present. I started to refine using NCS restraints with chain A as a
reference chain. Current Rwork/Rfree is 21/25. There is almost
On 19 May 2010, at 00:36, Paul Emsley wrote:
Jay Pan wrote:
Hello Everyone,
I have a reasonably well fitted electron density map through molecular
replacement. However, there is always some red region left no matter how
hard I tried when the mtz file is loaded into Coot. Is this because
The deposition 3fiy from the start of last year might be of interest:
FORMUL 2 NA199(NA 1+)
FORMUL 20 HOH *256(H2 O)
It is annoying that the periodic table offers such a discrete range of sizes
for 1+ ions; I hoped the lanthanide
One of the features that Global Phasing's routine runs of deposited PDB
structures often pick up is very close contacts between the SG of cysteine
residues and the CAB and CAC atoms of the propenyl groups on HEM ligands, not
described by LINK cards in the header of the deposited structure.
On Wed, 2009-04-01 at 14:33 -0700, Ethan Merritt wrote:
On Wednesday 01 April 2009 07:21:16 Thomas Womack wrote:
A perusal of the PDB reveals that the game of Periodic Table bingo still
has eleven rounds to run:
scandium, titanium, germanium, zirconium, niobium, neodymium,
dysprosium
A perusal of the PDB reveals that the game of Periodic Table bingo still
has eleven rounds to run:
scandium, titanium, germanium, zirconium, niobium, neodymium,
dysprosium, thulium, hafnium, bismuth and thorium remain absent from PDB
entries.
OK, many of these are elements that would rather be
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