Vriend
On 02/16/2015 10:58 AM, Tristan Croll wrote:
Dear all,
My apologies for the spam-like nature of my post, but I would like to draw your
attention to an important issue (outlined in an upcoming short communication to
Acta D, which will appear at doi:10.1107/S1399004715000826 once it's
Dear all,
My apologies for the spam-like nature of my post, but I would like to draw your
attention to an important issue (outlined in an upcoming short communication to
Acta D, which will appear at doi:10.1107/S1399004715000826 once it's online).
At present, neither the structural quality
CISPEP 4 ASP A 162GLY A 163 0-8.79
Which can be parsed/checked
but then again, who does?
https://www.youtube.com/watch?v=bAZqE2DnxUI
Best, BR
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tristan
Croll
Sent: Montag, 16. Februar 2015 10:58
.
Tristan Croll
Lecturer
Faculty of Health
School of Biomedical Sciences
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443
This email and its attachments (if any) contain confidential information
intended
What about nature's favourite cryoprotectant, trehalose?
From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK on behalf of Roger Rowlett
rrowl...@colgate.edu
Sent: Tuesday, 5 May 2015 7:22 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] cryo condition
We
A chemical component search through the Chemical Component Dictionary
(http://www.rcsb.org/pdb/ligand/chemAdvSearch.do) should get you there fairly
quickly. Just draw in the core amino acid N-CA(CB)-C=O and you should end up
with a pretty comprehensive list (although you'll need to handle
,
Tristan
Tristan Croll
Lecturer
Faculty of Health
School of Biomedical Sciences
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443
This email and its attachments (if any) contain confidential information
Might be worth trying to see if your protein will still crystallize in a
mixture of tris and TAPS buffer? The pKa of the latter is very close to tris,
but goes in the opposite direction with temperature - a roughly 3:2 TAPS:tris
mix should have minimal pH change on freezing.
Tristan Croll
.
Best regards,
Tristan
From: Tristan Croll
Sent: Tuesday, 17 February 2015 6:13 AM
To: wouter.t...@radboudumc.nl; CCP4 bulletin board
Subject: Re: [ccp4bb] Cis-peptide bond checking
Dear Wouter,
That does sound like a useful tool indeed - finding the proverbial
Sounds like a perfect application for principal components analysis. Check out
Bio3D: http://thegrantlab.org/bio3d/index.php.
Cheers,
Tristan
Tristan Croll
Lecturer
Faculty of Health
School of Biomedical Sciences
Institute of Health and Biomedical Engineering
Queensland University
There are a few visualisation packages out there that either have VR support
now or are very close to having it in place. I've personally had a chance to
briefly try out the Oculus Rift (aka seasickness simulator) in VMD. The
challenge with these things is doing the head-tracking,
I've often wondered about PEG (and, I guess, other synthetic polymers):
wouldn't it just be better to define the monomer, and then model a chain of
however many monomers you need?
T
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
Hi all,
While using the ccp4-jhbuild system to rebuild specific components on
the Mac, I'm running into the bug detailed at
https://bugs.launchpad.net/bzr-mac-installers/+bug/1244668 whenever 'bzr
info' is run. The workaround described there no longer appears to to
work for OSX Sierra.
Well, that's nice and straightforward. Thanks!
On 2017-02-16 10:15, Stuart McNicholas wrote:
I set DYLD_LIBRARY_PATH on the command line to point to location of
the svn libraries.
On 16 February 2017 at 10:09, Tristan Croll <ti...@cam.ac.uk> wrote:
Hi all,
While using the ccp4-j
Are these three crystals in order of harvesting (with different soaking times)?
How big is your ligand. How accessible is the binding pocket (and is there a
clear difference in accessibility between chains)?
T
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
Sorry - didn't realise that was going out to the whole list, and just
made a liar out of myself. Will bow out now.
On 2016-11-10 10:20, Tristan Croll wrote:
Hi Elton,
I certainly didn't say I agreed with their choice or thought it was a
good one. But as someone who grew up in a low-income
is now so prominent in our society?
Cheers,
Elton
On Nov 10, 2016, at 8:15 AM, Tristan Croll <ti...@cam.ac.uk> wrote:
In the interests of promoting understanding... the link below is to
an article on what is ostensibly a comedy website and contains a bit
of coarse language, but never
Phishing spam. Don't click.
T
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
> On 11 Dec 2016, at 17:45, Anindito Sen <andysen.to...@gmail.com> wrote:
>
> Guys
>
> are you all receiving the
Benzopinacol? It's sometimes used as the initiator for radical
polymerisations, so its presence in plasticware wouldn't be unheard of.
On 2016-11-27 10:33, Wei Liu wrote:
Dear all,
We have recently crystallized a recombinant protein produce from E.
coli, and determined the structure at 1.9 Å.
. Not sure if anyone sells
coverslip equivalents.
Best regards,
Tristan
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
> On 5 Apr 2017, at 04:19, Keller, Jacob <kell...@janelia.hhmi.org> wrote:
>
> Does anyone ha
*Ahem*
*ISOLDE
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
> On 13 Jul 2017, at 08:02, Tristan Croll <ti...@cam.ac.uk> wrote:
>
> This is more-or-less exactly the task I'm building ISODE for. It's early
>
This is more-or-less exactly the task I'm building ISODE for. It's early
days, still quite rough around the edges and by no means complete, but
if you have a machine with a decent GPU running a modern Linux distro,
then it's easily available as a plugin to ChimeraX after installing the
latest
This can be done in a few lines of script in any structural biology
package that provides a Python (or other) shell. Here's how I'd do it in
ChimeraX, for example:
Assuming your model is the only one loaded and atom names are all
standard:
m = session.models.list()[0]
histidines =
.
Cheers,
Tristan
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
> On 28 Apr 2017, at 18:33, Bernhard Rupp <hofkristall...@gmail.com> wrote:
>
> Dear Fellows of the Bond,
>
> when validating a QM r
noon.
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
> On 27 Apr 2017, at 10:26, Praveen Kumar Tripathi
> <tripathipraveen.i...@gmail.com> wrote:
>
> Dear all,
>
> sorry for off topic question.
>
> M
If I've got the site right (the equivalent to Asn833 in your image would
be Asn858 in 3rjo?) then the first thing I'd be checking is if you have
an unmodelled tail or loop that could be interacting here across a
symmetry interface. The dramatic kink in the helix there looks like an
asparagine,
Hmm... this is a bit of a philosophical pickle in my mind. Do we want to
model the structure as what it looks like after radiation damage has had
its way with it, or what it must have looked like *before* the damage? I
can see arguments both ways (and can sympathise with the former if you
want
on we know it's an
artifact of the data collection method, and we correct for known artifacts in
other contexts all the time.
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
> On 9 May 2017, at 17:49, Ian Tickle <ianj...@
as
expected. See figure 1 in http://molpharm.aspetjournals.org/content/70/5/1783.
Hope this helps,
Tristan
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
> On 21 Jun 2017, at 20:20, megha abbey <abbey...@gmail.com&
and deposit a new structure based on data from
an existing deposition, but it won't obsolete the old structure and I believe
it will only be accepted if accompanied by a peer-reviewed publication.
Hope this helps,
Tristan
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
With those statistics, it seems most probable that these two crystals
are the same protein. Do your two target proteins share an expression
system and/or purification protocol that could lead to the same
contaminant in both? If you have the resolution you could try Arcimboldo
to get an initial
. Have you tried asking
Phaser to search for two copies of your 57aa fragment?
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
> On 30 Apr 2017, at 23:26, Dr A.A. Jalan <aa...@cam.ac.uk> wrote:
>
> Dear all,
>
Peroxyacids are unlikely - they're very reactive/unstable under normal
conditions. Is it possible your crystal is just at unusually low pH so these
acids are protonated? That makes the carbon-oxygen bond lengths asymmetric,
possibly by enough to explain your blobs.
Tristan
Tristan Croll
Relying on refinement to fix cis peptide bonds for you is unlikely to
end well. It looks to me like you really need to spend some time
investigating and manually rebuilding these first.
On 2017-10-10 13:52, 师扬 wrote:
Dear all,
I am refining a model based on a 4.3A EM density map,and there are
Try http://www.glycosciences.de/modeling/sweet2/doc/index.php
Cheers,
Tristan
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
> On 30 Aug 2017, at 19:56, Reza Khayat <rkha...@ccny.cuny.edu> wrote:
>
> Hi,
>
&
You could try getting in touch with the authors of this:
https://www.ncbi.nlm.nih.gov/m/pubmed/26833545/.
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
> On 23 Sep 2017, at 19:05, Reza Khayat <rkha...@ccny.cuny.edu&
)
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
> On 28 Aug 2017, at 10:04, Johannes Sommerkamp
> <155b9e78396e-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Thanks a lot for your answers and the PyMOL mailing list
I should learn not to post while distracted. That last line was both
over-engineered, and wrong. What you want is:
rmsd = sum(numpy.linalg.norm(xyz1-xyz2, axis=1))/len(xyz1)
On 2017-08-28 14:32, Tristan Croll wrote:
In this case calculating the rmsd is easy:
- get the coordinates of each
it makes
perfect sense to provide a computational check for the (hopefully rare)
surprise case.
Best regards,
Tristan
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
> On 23 Nov 2017, at 19:35, r...@mrc-lmb.cam.ac.uk wr
Assuming you have a good reason for doing that, I'd suggest the best
approach would be to first generate a real-space map covering your
original coordinates, and then apply the transform to that. To transform
a volumetric map, all you're actually transforming is the (x,y,z)
coordinate of its
/711977?lang=en=GB).
Depending on your situation it may be feasible to do a single bulk synthesis
then click on a range of different groups after the fact.
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
> On 13 Nov 2017, at 21
This is quite straightforward in any package with a reasonable scripting
interface. In ChimeraX, for example:
-load your model
-make your selection
(https://www.rbvi.ucsf.edu/chimerax/docs/user/selection.html)
-open the shell (Tools/General/Shell), and in it, type:
from chimerax.core.atomic
Dear members of the structural biology community,
It is with great pleasure that I announce the release of version 1.0b1
of ISOLDE, a new, free for academic/nonprofit use, environment for
interactive rebuilding of macromolecular models against low-medium
resolution experimental
environments. Think of it
as having one carboxyl group protonated and H-bonding to the other, except that
the proton is more-or-less equally shared. Their most common role is as
pH-dependent conformational switches - very stably bonded below the pKa,
wanting nothing to with each other above.
Tristan
I've been quite impressed by ClusPro (https://cluspro.bu.edu) in the
past. Rather than pure rigid-body docking it makes some (pretty good)
effort to adjust interacting sidechains into reasonable arrangements.
The advanced options also allow you to specify attractions and
repulsions between
Yes it can. See 5x49 (residue 603) for a wonderful example.
On 2018-01-26 16:46, Michal Boniecki wrote:
I have positive density around lysine residue (image). This density is
found in all crystals, and only with this lysine. It is solvent
accessible but again not only this one is surface K
Looks like it could be a G-C dinucleotide?
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
> On 10 Jan 2018, at 04:09, Shankar Prasad Kanaujia <spkanau...@gmail.com>
> wrote:
>
> Dear All,
>
> Wish
Assuming you have a good reason for this, you can apply any arbitrary
transform fairly straightforwardly in ChimeraX. In the console
(Tools/General/Shell), and assuming your model is the only one loaded:
m = session.models.list()[0]
import numpy
transform_matrix = numpy.array([[r11, r12, r13,
Hi Careina,
This is a little confusing. A homology model *is* a set of coordinates
(usually provided as a PDB file by most servers/packages I know of). The
MolProbity site at http://molprobity.biochem.duke.edu/ allows you to
upload your own PDB file, and in my experience is quite forgiving
In all seriousness, it looks like it may be some form of hexose sugar?
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
> On 2 Nov 2018, at 21:14, Deborah Harrus wrote:
>
> Dear all,
>
> I came across an unidentif
Dear structural biology community,
I am very happy to announce that ISOLDE 1.0b2 is now available. All the
details including documentation are available on the new ISOLDE website
at https://isolde.cimr.cam.ac.uk, but the following is a short list of
new features and improvements since ISOLDE
In ChimeraX:
ctrl-click to select your atom, then in the command line below:
select zone sel
Best regards,
Tristan
On 2019-04-03 15:18, Stephen Cusack wrote:
Dear All,
I am looking for an accessible programme that allows selection of
atoms from a PDB file
within a sphere of inputted
In ChimeraX, you can promote a selection to whole residues with:
select up
Repeating the command will expand to whole secondary structure elements,
then whole chains, then whole models. You can reverse this with:
select down
On 2019-04-03 16:13, Gianluca Santoni wrote:
I could be useful
Dear Tereza,
First, a shameless plug for ISOLDE (https://isolde.cimr.cam.ac.uk). It’s built
specifically for working with models around your resolution.
Other than that, I’d suggest having a close look at the corresponding sites in
your high-resolution reference models as a sanity check.
Hi all,
I’m trying to find an authoritative list of all obsolete residue IDs in the
CCD, but I’m coming up blank. Ligand Expo will tell me if a given ID is
obsolete, but where is this information stored? Components.cif includes an
“Obsoleted” date for a few dozen residues, but that doesn’t
I've been really happy with the performance of my laptop (a 2016-era
Asus ROG Strix GL502vs) for MD work. It's a gaming model (GTX 1070
rather than Quadro, and an i7 CPU), but it's solid and seriously
powerful. I dual-boot Fedora and Windows (I initially tried with Ubuntu,
but its setup
It turns out the field I was looking for is
_chem_comp.pdbx_release_status. Thank you very much to those who pointed
me to this!
On 2019-02-08 22:31, Tristan Croll wrote:
Hi all,
I’m trying to find an authoritative list of all obsolete residue IDs
in the CCD, but I’m coming up blank. Ligand
Seems to be working fine:
https://downforeveryoneorjustme.com/molprobity.biochem.duke.edu. It's
not a secure site, though: https://molprobity... times out, whereas
http://molprobity... goes through. Could that be your issue?
On 2019-06-04 13:19, Andrea Pica wrote:
Hi everyone,
it seems that
Dear structural biology community members,
I am happy to announce that ISOLDE 1.0b3 is now live and available for
installation via the ChimeraX Tool Shed. To get it, just download,
install and run the ChimeraX 0.9 release version from
Everyone keeps telling me I look terrible, but I'm unphased...
On 2019-08-15 12:42, Gerard DVD Kleywegt wrote:
Dear CCP4BB-ers,
Once again I turn to you in my hour of need. I *urgently* need a
side-splittingly funny, and ideally punny, structure-related
sentence/statement/claim/expression to
... although this raises a question: if there are no free reflections,
then why is a "Rfree" score being reported at all?
On 2019-08-30 16:53, Christian Roth wrote:
No. As pointed out by Pavel, there are no reflections flagged as
"free reflections" used to calculate Rfree. Therefore you don't
Hi all,
Since the release of ISOLDE 1.0b3 I've begun releasing regular
(weekly~fortnightly) development builds of ISOLDE. These are built
against the ChimeraX daily build at the time of release - if you
download a ChimeraX-daily build and install ISOLDE in the usual way via
Tools/More
I couldn't resist doing a little playing with 6mo0 in ISOLDE. The
sequence past Gly1151 is wrong - after jumping a small gap (density
clearly indicates a single missing residue here), it continues on from
1165. Corrected the following sequence to GVVTRS, deleted the ligands,
did some basic
Hi Radu,
Barring some truly spectacular advances, I think that crystallography is
going to have a major role to play for a long time yet. Looking at
single-particle cryoEM, for almost every target apart from the few
ultra-rigid "rocks" the reconstruction will have a wide range of
resolutions
For that matter, the insulin *receptor* is a spectacular example of very
large conformational changes in a homodimer.
On 2019-10-09 15:27, Eleanor Dodson wrote:
There are many insulin structures with domain shifts.
4ins and 1trz share sequence but have different conformations for one
of the
Just to add to the already-excellent list of replies, this can also be done
quite straightforwardly with the Clipper plugin in ChimeraX. I’d be happy to
provide an example script if you want one.
Best regards,
Tristan
> On 12 Jan 2020, at 18:54, orly avraham wrote:
>
> Hi Marcin,
>
>
Happy new year to all my colleagues in the structural biology community!
I'm delighted to announce the release of ISOLDE 1.0b4 to coincide with
the stable release of ChimeraX 0.91.
What is ISOLDE?
ISOLDE is a plugin to UCSF ChimeraX, designed to ease the task of
macromolecular model building
Hi all,
For those still lucky enough to be working on molecular model building
during this crisis, I've just pushed ISOLDE 1.0b5 out to the ChimeraX
ToolShed (to work with the ChimeraX 0.93 release version - download from
http://preview.cgl.ucsf.edu/chimerax/download.html#release, then
I once knew a particularly germaphobic IT manager who used to absolutely
*everything* via ssh or remote desktop from his own laptop, even when he
was physically in front of the user's computer. If feasible, that
approach would actually seem quite smart in the current environment.
On
Posted semi-seriously (they look like they’d be awful to use, but maybe I’m
being pessimistic): https://wiki.ezvid.com/best-virtual-keyboards. With a
projection keyboard, all you have to worry about cleaning is the benchtop.
> On 29 Apr 2020, at 21:38, Crissy Lynette Tarver wrote:
>
>
For what it’s worth, I’ve spent the last few days going over most of the
existing COVID-19 related structures and rebuilding/re-refining wherever I
considered necessary. The resulting models along with some basic explanatory
notes are at
You got off lucky. An old friend of mine learned this lesson when on a
particularly sunny day he spent an hour out on a New Zealand glacier in
shorts with no underwear...
On 2020-05-06 16:17, James Holton wrote:
I feel I should correct you on one thing Tim: UV _can_ go around
corners because
I'd like to append a very important caveat to this discussion: most of the talk
on Rfree as protection against overfitting is perfectly correct, if your
dataset is high enough resolution. Remember that Rfree only provides protection
against one form of overfitting: that is, fitting of atoms
The isolde suggestion already made is an excellent one. The hardest part of
that is getting the right version of chimeraX working. But, once you've done
that its pretty straightforward.
Hopefully not for too much longer. All going well, ISOLDE 1.0 (to work
in ChimeraX 1.0) should be out
Thermo Fisher sells His-tagged GFP quite cheaply.
https://www.thermofisher.com/order/catalog/product/A42611#/A42611
Tristan
On 2020-07-02 10:31, Mark J van Raaij wrote:
Dear All,
Wondering if anyone knows of an economical commercial source of a soluble His-tagged protein. In principle any
B, C,
Ag1, Ag2, Ag3", then we have something that is far more immediately accessible
to the user.
From: Dale Tronrud
Sent: 04 December 2020 17:01
To: Tristan Croll ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data
equire ongoing improvement ("remediation") to
ensure consistency, accuracy, and overall quality.
www.wwpdb.org
From: Greg Couch
Sent: 04 December 2020 18:51
To: Luca Jovine ; Mailing List CCP4 ;
Mailing List PDB,
Cc: Tristan Croll
Subject: pdb-l: Re:
aking decisions like this.
From: Dale Tronrud
Sent: 04 December 2020 18:16
To: Tristan Croll ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB --
N-glycans are now separate chains if more than one residue
Creating meaning in the
To go one step further: in large, heavily glycosylated multi-chain complexes
the assignment of a random new chain ID to each glycan will lead to headaches
for people building visualisations using existing viewers, because it loses the
easy name-based association of glycan to parent protein
This is a number that needs to be interpreted with some care. 2 Å crystal
structures in general achieve an RMSD of 0.2 Å on the portion of the crystal
that's resolved, including loops that are often only in well-resolved
conformations due to physiologically-irrelevant crystal packing
... and of course I meant "between model and target".
____
From: Tristan Croll
Sent: 08 December 2020 16:35
To: CCP4BB@JISCMAIL.AC.UK ; Marko Hyvonen
Subject: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less
pipetting (?)
I'm not Randy, but I do have an answer: like this. This is T1049-D1. AlphaFold
prediction in red, experimental structure (6y4f) in green. Agreement is close
to perfect, apart from the C-terminal tail which is way off - but clearly
flexible and only resolved in this conformation in the crystal
Hi Prem,
The immediate problem here is that the curve for the processed substrate simply
cannot be described by simple Michaelis-Menten kinetics. Assuming the assay has
worked as expected, the declining rate with increasing substrate concentration
suggests to me that this substrate also acts
Hi all,
I'm very happy to announce the release of ISOLDE 1.2, now available for
installation into the ChimeraX 1.2 release. To get it, first download and
install ChimeraX 1.2 from https://www.rbvi.ucsf.edu/chimerax/download.html,
then go to "Tools/More Tools..." in the menu and follow the
(sending properly this time, rather than just to Rasmus)
I don't believe a "color by RMS" option is in ChimeraX right now (I'll suggest
it to the developers), but this will align all models then set B-factors for
each residue to the RMS CA deviation from the mean position. Could be extended
Hi Faisal,
This is really a question for the ChimeraX-users list
(chimerax-us...@cgl.ucsf.edu). But the quick run-down: using the File/Save
dialogue, you'll see a checkbox with "Save relative to model: " and then a
drop-down menu. Just choose the map in the drop-down menu, and you should get
Hi Faisal,
Are you using the latest version (1.2.5)? That should give you a dialog that
looks something like this.
Best regards,
Tristan
[cid:c60bb51b-6f11-4646-9800-6ce976abc3f0]
From: khaja faisal tarique
Sent: 28 June 2021 10:29
To: Tristan Croll
Cc
.
-- Tristan
From: Jon Cooper
Sent: 28 June 2021 13:43
To: Tristan Croll ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] saving coordinates with respect to map in ChimeraX
It's not important, but I am curious what 'Save relative to model/map' actually
means in that widget
Hi all,
If I open (as far as I can tell) the mmCIF for any structure in the wwPDB that
contains both defined amino acids and UNK in the same chain, then the UNK
section is treated as covalently bonded to the flanking sequence. This appears
to be a bug in the mmCIF generation itself, not in the
I know . Just suggesting the most likely cause of the problem.
-- T
From: Bernhard Rupp
Sent: 06 February 2021 14:38
To: Tristan Croll
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] ideal ligands
That is what 'uranium atom solution' implies:
All atoms
The ideal coordinates in the CCD entries for BCR and LUT are null - my guess is
that in these cases all the coordinates just default to (0,0,0) in the PDBeChem
script.
From: CCP4 bulletin board on behalf of Bernhard Rupp
Sent: 05 February 2021 20:51
To:
D. Jeffrey
Sent: 12 February 2021 19:56
To: CCP4BB@JISCMAIL.AC.UK ; Tristan Croll
Subject: Re: Bug in mmCIF handling of UNK residues?
Doesn't seem to be the case for all instances: that table isn't present in 5BV0
despite the N-terminal residues of Nyv1 being modeled as UNK in the
Vps16:Vps33
I agree with Dale. Tools like MolProbity are not the right approach to
validating a structure prediction. To understand why, just consider that all
you need to do to get a perfect MolProbity score is predict every structure as
a single long alpha helix with ideal rotamers, with a kink at each
Hard but not impossible - even when you *are* fitting to low-res density. See
https://twitter.com/crolltristan/status/1381258326223290373?s=21 for example -
no Ramachandran outliers, 1.3% sidechain outliers, clashscore of 2... yet
multiple regions out of register by anywhere up to 15 residues!
I've seen this happen with B-factor refinement reasonably often. As I
understand it the basic problem is that for small B-factors the gradient
d(density)d(B) is large, but for large B-factors the gradient is small. So if
the starting B-factor on an atom is very low and substantially lower than
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