Hi Miha,
I thought the PDB actually uses DSSP. Perhaps it is a different version,
there have been some new releases recently. Anyway, there is no reason why
you should stick to the assignment of the PDB. If another program gives
slightly different results you can use those as long as you make
Hi Bernhard,
The formula from Tickly applies to the weighted/generalized/Hamilton free
R-factor. From k-fold cross validation tests we observed that the 'regular'
R-free has a standard deviation of R-free*(Nref )^-1/2
Cheers,
Robbie
-Original Message-
From: CCP4 bulletin board
HI Sue,
Can you give rmsZ for the bond and angles (from the Refmac output)? I never
could figure these rmsd values out...
I'm guessing that the restraint are too loose, or at least not optimal.
Perhaps, they went overboard with the TLS as well (sometimes fewer TLS goups
give much better R and
Hi Herman,
Tighter restraints typically close the gap between R and R-free. This does
not mean one should just tighten the restraints to satisfy one's own (or a
referee's) idea of what the gap should be. I don't think there is a clear
target of how large or small the gap should be. If you
-off in REMARK 2 or 3
lower than the maximal resolution of your reflection file, it will
automatically use paired refinement to find the best resolution cut-off (yes,
this is a self-plug!).
HTH,
Robbie Joosten
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
In Windows:
findstr /b /v ANISOU input.pdb output.pdb
Cheers,
Robbie
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Tim Gruene
Sent: Tuesday, June 11, 2013 10:40
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fwd: [ccp4bb] pdbset
Rachel Kramer Green, Ph.D.
RCSB PDB
kra...@rcsb.rutgers.edu
Twitter: https://twitter.com/#!/buildmodels
Facebook: http://www.facebook.com/RCSBPDB
On 5/24/2013 12:41 PM, Robbie Joosten wrote:
Perhaps a silly question: will old entries with SPLIT records
Perhaps a silly question: will old entries with SPLIT records be superseded by
consolidated entries? And what about entries split for other reasons than size
(there are only a few of those, and they are old)?
Cheers,
Robbie
Van: Gerard DVD Kleywegt
Verzonden:
Hi Eleanor,
The recent versions of Refmac work well with the records in PDB format.
According to the list of bug fixes on the website, Refmac should now take
the distance from the PDB file (it used to complain about the distance
record). Changing the 1.48 to 1.61 in the new LINK record should
Hi Patrick,
Did you try using a different refinement program (e.g. Refmac)? Which type
of NCS restraints did you use, global or local (torsion- or distance-based)?
Have you tried optimizing your restraint weights? Have you tried running a
huge number of refinement cycles? You can also try running
Hi Markus,
You could try changing your Refmac version. The version you are using is
ancient. You may have an old version in your PATH next to the new one because
your CCP4 seems up to date.
AFAICT there is nothing wrong with the LINKR or the HETATM records
Sent from my Windows Phone
Hi Kavya,
Which validation program did you use? How big is the deviation (in sigma
values)? Is it the only outlier? What is your overall bond angle rmsZ?
Using external restraints is a bit over the top here, especially if it is the
only outlier. If your rmsZ is high (close to or over 1) then
Dear Kavya,
First try Herman's suggestions. You can try changing the restraint weight but
it will probably not solve the problem; it may hide it. If you cannot solve the
problem and you did the best you can do, you can deposit the model with the
outlier. The PDB does not reject models with
, 2013 23:03 BST Robbie Joosten wrote:
Hi Martyn,
A shame then that these 'helpful' annotators did not make use of
Pavel's basic sanity on the space group (*mentioned below) and check
back to the one listed in the uploaded PDB file.
As far as I know, EDS is run on all new depositions at PDBe
is not twice as large as
published one
would entirely suffice -:)
Pavel
From: Robbie Joosten robbie_joos...@hotmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Friday, 12 April 2013, 22:57
Subject: Re: [ccp4bb] Puzzling Structure
Waters are moved during
Waters are moved during annotation using the perceived space group's
symmetry operation. So if the authors give the wrong space group, then the
annotation pipeline understandably messes things up. If the originally
uploaded PDB file was kept by PDBe, then the problem can be recovered quite
easily
Hi Tim,
I don't think the 5-10% or 500-1000 reflections are real rules, but rather
practical choices. The error margin in R-free is inverse proportional with
the number of reflections in your test set and also proportional with R-free
itself. So for R-free to be 'significant' you need some
anymore in favour
of
R_meas...
Cheers,
Tim
On Tue, Mar 26, 2013 at 10:24:51AM +0100, Robbie Joosten wrote:
Hi Tim,
I don't think the 5-10% or 500-1000 reflections are real rules, but
rather practical choices. The error margin in R-free is inverse
proportional with the number
Dear Sonali,
There is no such thing as an ideal rmsd for bonds and angles given resolution.
IMO you should use rmsZ which also doesn't have an ideal value. If its below 1
your good. As for the isotropic vs anisotropic, you can use a hamilton test if
you do two refinements changing only the
Small addition to Ian's comment. The value you give with 'weight auto $value'
is a starting value. Refmac will gradually change it if needed (it's
autoweighting after all) and your starting value does matter somewhat. Based on
Ian's advice PDB_REDO uses a starting value of 2.50 which seems to
Btw, the book is good reading.
Best, BR
-Original Message-
From: CCP4 bulletin board
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Robbie
Joosten
Sent: Tuesday, March 12, 2013 10:03 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb
Dear Srinivasan,
Although the Twilight program can only look at deposited PDB entries, the
tips about ligand validation in the paper are very useful. I suggest you
start from there.
You can use EDSTATS in CCP4 to get real-space validation scores. Also look
at the difference map metrics it gives
Hi Tim,
Our approach is a bit different. We first try to establish whether the
R-free set is biased, by checking whether R-free is surprisingly low
compared to R given the data parameter ratio. If this is the case (or if we
chose a new R-free set for some reason, e.g. because it was too small)
Hi Folmer,
Just to add some tips:
Concerning the naming as one molecule: the sugar monomers get the same
chain ID as the protein they are connected to and arbitrary residue
numbers.
I usually start numbering from 1000 to prevent overlap with the numbering
of the amino acids.
1) Just don't
;-)
The glycosciences.de link is really useful. There does not seem to be a
test to
verify correct PDB nomenclature though. Or perhaps RAF (for raffinose, a
tri-
saccharide) is OK to use?
Best regards,
Folmer
2013/2/21 Robbie Joosten robbie_joos...@hotmail.com
Hi Folmer
Hi Ian,
The warning refers to a MET 59 in chain A whereas you only have MET 72. That
is very suspicious. Non-sequential residues further apart than x Angstrom
automatically get a gap record. Have you tried a newer version of Refmac,
because this feature was added quite a while ago?
What is your
renumber
any LINK, SSBOND CISPEP records as I do) so it would have the same
problem.
Cheers
-- Ian
On 18 February 2013 17:09, Robbie Joosten robbie_joos...@hotmail.com
wrote:
Hi Ian,
The warning refers to a MET 59 in chain A whereas you only have
MET 72
Hi Ed,
This is a 'compatability' option in Refmac that internally renames atoms. If
you comment out 'MMA .C7 CM' in your mon_lib_list.cif file,
the problem will disappear.
Cheers,
Robbie
Date: Sun, 10 Feb 2013 23:35:25 -0500
From: epozh...@umaryland.edu
Subject:
On Mon, 2013-02-11 at 09:56 +0100, Robbie Joosten wrote:
This is a 'compatability' option in Refmac that internally renames
atoms. If you comment out 'MMA .C7 CM' in your
mon_lib_list.cif file, the problem will disappear.
Robbie,
thanks a lot - this fixes
Just to add some more possibilities:
- You can download maps from EDS or models and maps from PDB_REDO straight into
CCP4mg.
- You can download PDB_REDO maps and models into PyMOL using this plugin
(http://www.cmbi.ru.nl/pdb_redo/pymol.html) for which we should thank Ed
Pozharski. Note that
Note that we discuss rmsZ values in the paper, not rmsd. This is done on
purpose; rmsd values do not take the standard deviation of bond lengths into
account. This makes it needlessly difficult to compare values.
Consider reporting rmsZ instead of rmsd.
Cheers,
Robbie
Sent from my Windows
Hi Nat,
DSSP recently went open source with a very liberal license. So you can consider
using the real DSSP now. This may also be the moment to integrate DSSP in CCP4.
Cheers,
Robbie
Sent from my Windows Phone
From: Nat Echols
Sent: 2013-01-28 17:32
To:
of running 10.5 to test this. If it doesn't work, please send
me the output so I can try to infer the required extra changes.
best regards,
-maarten
Van: Robbie Joosten [robbie_joos...@hotmail.com]
Verzonden: zaterdag 26 januari 2013 10:16
Aan: Maarten Hekkelman
Hi Ed,
I've had this problem as well. It's the result of the very small R-free set
fraction. There is an error routine that catches really small R-free sets,
but 0.5% gets through and triggers ar problem. My workaround is to just use
a larger R-free set fraction (more than 1%).
The version number
I noticed that Refmac has done the 1vs0 thing correct for ages, which is very
useful because mix-ups between the work set and test set used to be quite
common in the reflection files at the pdb (Refmac saved me a lot of extra work
with this). Dealing with this problem is very simple as the
Dear Urmi,
The way you switched from Phenix to Refmac may not have resulted in the flat
B-factor model in Ethan's paper. You should really do a thorough test in which
you reset the B-factors before you start refinement. Shameless plug: PDB_REDO
will do this automatically and has a few fallback
Hi Supratim,
The clashscore gives the relative number of clashes, not their severity.
This makes it difficult to see what your specific problem is. Sever clashes
(with large overlaps) are usually the result of errors in your model and
need individual attention. Light bumps can usually be solved
Hi Douglas,
Using two Table Is is a good way to show the difference between the two
cut-offs, but I assume you will only discuss one of the models in your
paper. IMO you only need to deposit the high res model, so there should be
no problems with resolution conflicts in the PDB file. The
Hi Ian,
It's easy to forget about LINK records and such when dealing with the
coordinates (I recently had to fix a bug in my own code for that).
The problem with insertion codes is that they are very poorly defined in the
PDB standard. Does 128A come before or after 128? There is no strict rule
. In practice, as Ed pointed out, it is a big mess.
Cheers,
Robbie
-Original Message-
From: Ian Tickle [mailto:ianj...@gmail.com]
Sent: Wednesday, December 05, 2012 17:26
To: Robbie Joosten
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] thanks god for pdbset
I had always assumed
, 2012-12-05 at 17:02 +0100, Robbie Joosten wrote:
Hi Ian,
It's easy to forget about LINK records and such when dealing with the
coordinates (I recently had to fix a bug in my own code for that).
The problem with insertion codes is that they are very poorly defined in the
PDB standard
Hi Jim,
The speed at which the B-factor converges depends on many factors. The B-factor
restraint weight that Herman and I mentioned (the one you should optimise
before changing occupancies!) is an important factor. Also the position of your
atomic coordinates WRT where they should end up is
Hi Grant,
This is part of the recurring side chain discussion. There is no consensus in
the community about what the optimal approach is.
In your current approach you are adding a model parameter (occupancy) to
improve the fit with the experimental data (remove negative difference
density).
Hi Meindert,
The PDB will let you do what you want and as a result there are a few PDB
entries with crazy residue numbering. I would use insertion codes only for
real insertions or engineered linkers. Like Nat said, they are a nightmare
for many programmers which is why they are poorly supported
is an
underestimate because the B-factor model used wasn't stored properly for the
older entries. If more accurate numbers are needed, they can be mined from the
PDB_REDO databank.
HTH,
Robbie Joosten
Netherlands Cancer Institute
www.cmbi.ru.nl/pdb_redo
Date: Thu, 11 Oct 2012 12:17:39 -0700
From
that. Shameless plug: PDB_REDO
has such an automated procedure.
HTH,
Robbie Joosten
Date: Wed, 3 Oct 2012 03:19:48 +0530
From: faisaltari...@gmail.com
Subject: [ccp4bb] ideal rms bond length
To: CCP4BB@JISCMAIL.AC.UK
Dear all
i request you to please answer my basic query about the ideal
to PDB_REDO's strict criteria anisotropic B-factors are
acceptable in two thirds of the cases. This was tested with Refmac on 285 PDB
entries; ShelX's new restraints may well increase the success rate.
HTH,
Robbie Joosten
Netherlands Cancer Institute
www.cmbi.ru.nl/pdb_redo
-Original Message
Dear Norman,
Refmac version 5.0 sounds unlikely, the version with CCP4 6.3 is 5.7.0029.
Anyway, your DNA seems to have asterisks in the atom names, which is 'so last
decade' (they were removed in 2008). Refmac and Coot may not be equally
forgiving for legacy formats. IMO neither should be. The
maintainers because I’
m not sure this service is public yet. You can also cheat a bit and just get
the HSSP for the closest homologue in the PDB.
HTH,
Robbie Joosten
Netherlands Cancer Institute
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ??
Sent: Wednesday
Hi Faisal,
It looks like your restraints are simply not tight enough. Try optimizing
the restraint weight. You should also run more cycles of refinement to make
sure it converges.
The initial gap between R and R-free is pretty small. Did you do much
refinement before this run?
Cheers,
- From: CCP4 bulletin board
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie Joosten Sent:
Thursday, 12 July 2012 12:16 a.m. To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Chiral volume outliers SO4
Hi Ian,
@Ian: You'd be surprised how well Refmac can flatten sulfates if
you have
...@mail.cryst.bbk.ac.uk]
Sent: Friday, July 13, 2012 14:09
To: Robbie Joosten
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Chiral volume outliers SO4
Dear Robbie and ccp4bb,
Is 1N1 not a different type of problem though, where a chirality restraint
is
valid and so the atom labelling
Hi Joel,
I prefer the swapping of atom names, which is pretty much what the program
chiron does, over hacking the restraint file. The latter makes the problem
reappear as soon as you use your PDB file on a machine with an 'unhacked'
restraint file.
@Ian: You'd be surprised how well Refmac
Hi Ian,
@Ian: You'd be surprised how well Refmac can flatten sulfates if you
have a chiral volume outlier (see Figure 1d in Acta Cryst. D68: 484-496
(2012)).
But this is only because the 'negative' volume sign was erroneously used
in
the chiral restraint instead of 'both' (or better
Dear Regina,
Re. 2) Which program gave the virus warning? Internet Explorer warns about
executable files that are not downloaded frequently. This warning can usually
be ignored (I got a similar warning for a nightly build of Coot yesterday). If
your antivirus program gives a warning I'd be
Hi Ed, If you are looking for a specific protein, why not get all PDB files
with a DBREF record pointing at the uniprot record of the protein you want? You
can do a simple text search in the PDB, e.g. 'MYG_PHYCA'. Cheers,Robbie
Date: Fri, 22 Jun 2012 22:39:12 -0400
From:
Hi Tim,
With small test sets, R-free doesn't become meaningless you just have to take
into account that R-free has an error margin which is higher than for cases
with a large test set.
Few people report this error margin, but with a small data set you can easily
do K-fold cross validation.
Hi Uma,
How different are your NADs optimised in Refmac and Coot? Are you sure you are
using the same geometric restraints? Coot has to know where Refmac's restraint
files are. This info is passed through an environment setting on your computer
(I don't know the name by hart. Anyone?). Are you
Quasi on-topic rant:
I would advice against using the 'both' option for any well defined ligand.
It's a hack to avoid thinking about which atom belongs where and it allows you
to be inconsistent. This makes it difficult for others to use your model,
because aligning atoms of ligands becomes
Hi Uma,
The optimal weight is indeed resolution dependent, but hard to predict. In
Refmac you can follow LLfree when you optimize the restraint weight and also
keep an eye on the gap between R and R-free (it should not be too wide). Like
Rob said, your geometry should be 'reasonable'. This
available at
http://www.cmbi.ru.nl/pdb_redo/others/3k78.tar.bz2
Our apologies to those who have looked for this entry in vain.
Best wishes,
Robbie Joosten (on behalf of the PDB_REDO team)
Biochemistry
Netherlands Cancer Institute
P.S. The whole fraud thing seems to have interfered with the annual
Hi Everyone,
Pavel’s statement is likely a bit of an exaggeration, but he has a valid (yet
hard to prove point). The default in CCP4i was (and is?) to use hydrogens only
if present in the input file. This is IMO not a safe default.
Because there were some reporting errors in the past
Hi Dialing,
Most water picking tools are rather overenthusiastic and end up placing some
waters at places where they should not be. This causes some overfitting and
an increase of R-free. I'm hideously old-fashioned and recommend
conservatively building waters by hand.
There are some good
Hi Frank,
EDS already does that. Even so, reproducing the R-factor does not prove that
the map is reliable. See for instance 3frk for which the deposited dataset
is much smaller and less complete than the one used for refinement. The map
from EDS is therefore completely model biased.
I only
Hi Phil,
It is annoying problem especially for Phe and Tyr which have standard
rotamers close to the critical chi angles (-90 and +90). Asp and Glu do not
have standard rotamers near critical angles, so the problem should be much
smaller (but I still get them too often). If Val, Leu and Arg
(and it is if it is not and is merely an issue of nomenclature (as I
suspect is the case)). So the question is, if the problem is indeed one of
nomenclature, what software (if any) described it as a chirality issue? If it
is one of ours we should fix that.
Paul
On 05/01/12 11:44, Robbie Joosten
Hi Afshan,
Just swap the (names of) the CD and CG atoms, no need for refinement. The CCP4
dictionary allows both chiralities for LEU and VAL, so Refmac won't detect the
problem. The problem is still very real to many programs so it should be fixed.
Cheers,
Robbie Joosten
Date: Thu, 5 Jan 2012
Hi Matt,
WHAT_CHECK writes out a file called check.db that contains per-residue scores
for several quality metrics. It is fairly easy to parse.
Cheers,
Robbie
Date: Thu, 8 Dec 2011 23:08:45 -0500
From: mattw...@gmail.com
Subject: [ccp4bb] How to assess geometry in a model?
To:
Hi Florian,
There are quite a few tools that do this check for you. To name a few: WASP
(old but good, build the ion as water), WHAT_CHECK
(http://swift.cmbi.ru.nl/servers/html/index.html), Check My Metal and
probably quite a few others. All of them use the bond valence sum, but they
all have a
Hi Aaron,
You don't explain why you have so few reflections. Is it a small cell, low
resolution or just really bad data?
Assuming it's not the last one and your data is reasonably complete, I would
try this:
- Divide your reflections into six groups (and check that these
groups
Hi James,
That is not exactly a lot of info to decide the best weight. The optimal
weight is (very loosely) resolution dependent. At normal resolutions the
optimal matrix weight is usually well below 1.0. Start at 0.3 and try a few
weights to see what works best for your data. To close the
Hi Kenneth,
This looks like an off-by-one bug in the restraint generation. Typical sources
are weird LINKs, wrong atom names and bad luck. I suggest you make sure you
have the very latest Refmac and dictionary and try setting up a new refinement
instead of recycling an old job. If that doesn't
Hi Francis,
Even though they are not published, there are enough models in the PDB for
which reevaluation of the crystallographic data leads to new biological
insight. Unfortunately, a lot of the insight is of the type that ligand
doesn't really bind, or at least not in that pose. Another nice
Hi Ed,
This is a follow up (or a digression) to James comparing test set to
missing reflections. I also heard this issue mentioned before but was
always too lazy to actually pursue it.
So.
The role of the test set is to prevent overfitting. Let's say I have
the final model and I
One would assume that Windows software would read DOS/Windows type text
files...
Open the file in Wordpad. Unlike Notepad, it is able to work with Windows and
Unix type text files. If you edit something and save the file, it will be in
Windows style. If Superpose stops on that, it should
Dear Protein Chemistry (?),
When R and R-free drift off you are probably refining with suboptimal weights.
If anything, it proves you still have work to do. At convergence R and R-free
do not really change anymore so neither does the difference. If you have
already done a lot of rebuilding and
Hi Dale,
The data looks fine but the refinement for 3kj5, 2qns's 'improved' model, is
still pretty poor. Looking at the EDS maps for this entry there is some (model
bias) density for the ligand but, it is clearly not there. The PDB_REDO
optimization
Dear Li(?),
The MolProbity server fixes the atom naming before the actual validation. You
can use that. The ATOM/HETATM conversion is not needed, the PDB will do that
for you when you deposit your structure model. If you really need it now, I
guess it's easy enough to do with you favourite
-
The link from that page is dead...and an inquiry to the webmaster
bounced. Anyone know where WASP is now?
Thanks
Christina
Oklahoma State University
From: Robbie Joosten robbie_joos...@hotmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, August 2
Dear Young-Jin,
If you model it as water, you can use WASP. It's an old program but still
accesible here: http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl
Cheers,
Robbie
Date: Tue, 2 Aug 2011 14:24:09 -0400
From: yj...@brandeis.edu
Subject:
Jung-Hoon,
This is a so-called WaReZ request, which could get you banned a lot of webfora.
Of course, we are all guilty of it at some occasions. The best way to get an
article is to ask the authors, they are allowed give away free copies
(depending on the journal I guess). Hooray, for authors
Hi Kim and Kevin,
Even then you can have chirality inversions during real-space refinement, which
would destroy the SWEET input model from. There is no substitute for common
sense (and validation) here.
That said, Kevin, something to autobuild carbohydrates (given a sequence) would
be
Hi Brittney,
DNA is pretty standard so the restraints should be in the dictionary. Perhaps
the DNA in your model has non-standard residue names (PDBv2). Are your bases
called DT, DA, etc? Do your atom names have * or '?
Cheers,
Robbie
Date: Tue, 26
Hi Artem,
Thank for that nice example of a protein structure used to pimp a movie. Ribbon
representations are always the scariest.
Cheers,
Robbie
Date: Sat, 16 Jul 2011 10:57:21 -0500
From: artem.evdoki...@gmail.com
Subject: [ccp4bb] unusual sighting of a crystal structure
To:
Hi Ed,
I was recently looking for that value myself, but couldn't find it. I suppose
(at some point) it may be useful information to deposit. If something is a mean
value, it is nice to know how many individual values were used to construct
that mean. Unfortunately, there doesn't seem to be
Hi Careina,
Assuming you don't suffer from a very poor data parameter ratio that would lead
to such a large R-free/R, you need to improve your refinement. If you have NCS
you should use local NCS restraints. You could also try jelly-body restraints,
although they may not work at your
function in refmac5.6?
2011/7/9 Robbie Joosten
robbie_joos...@hotmail.commailto:robbie_joos...@hotmail.com
Dear Qixu,
refamac 5.6 works well at these resolutions. You can add commands to
your refinement in CCP4i by using the 'Run and view command script' (or
something like
Dear Qixu,
refamac 5.6 works well at these resolutions. You can add commands to your
refinement in CCP4i by using the 'Run and view command script' (or something
like that) option and just typing in the extra commands. Jelly-body has worked
very well for me (although I use tigheter
Subject: Re: [ccp4bb] low resolution refinement
To: robbie_joos...@hotmail.com
CC: CCP4BB@jiscmail.ac.uk
Hi,
Thank you for your suggestion.
Could you tell me what is riding hydrogens?
And it seems there is not reference model function in refmac5.6?
2011/7/9 Robbie Joosten
Dear Petr,
Did you try WHAT_CHECK? It has a number of tests for water and will take
indirect interactions with the macromolecule into account.
Cheers,
Robbie
Date: Wed, 22 Jun 2011 16:01:45 +0200
From: arnaud.goepf...@unibas.ch
Subject: Re: [ccp4bb] Waters in ADIT
To: CCP4BB@JISCMAIL.AC.UK
are must-use tools for that. Coot also has many
usefull features for validation. Good luck. Cheers,Robbie Joosten
For the record:-UNK is for unknown residues only. That means that you know that
you are looking at an amino acid you just don't know which. You should assign
element types. It used to be defined to CB (just like ALA), it now goes to CG.
I don't see the point of this update.-UNL is for unknown
Hi Wolfram,
This was an early study on the subject:
http://www.ncbi.nlm.nih.gov/pubmed/8594192
The software is still accessible via the STAN server.
Cheers,
Robbie
Date: Tue, 14 Jun 2011 17:51:21 -0400
From: wtem...@gmail.com
Subject: [ccp4bb] non-waters among structured solvent atoms
Hi Ethan,
I also reset the temperature factors to 20 at
the beginning of each refinement round. The refinement resolution is 75
to 1.8 A, and the space group is C2, if it matters.
I am virtually certain that refinement of individual anisotropic
U^ij terms cannot be justified at 1.8A.
Macromolecular Structure Group
Dept. of Biochemistry and Biophysics
University of California, San Francisco
On 2011-05-04 05:32, Robbie Joosten wrote:
Hi Darren,
Thank you for the link. It may be a usefull tool. Unfortunately, the
site was buggy in IE9. It worked much better in FF4
Hi Ed,
Personally I don't care one way or the other, but it may be pointed out
that if D25 is actually number 37 in a homologous protein, it should be
D37. Just as acknowledgement of the (somewhat purist) point of view
that the residue number should denote its linear distance from the
Hi Everyone,
Does anyone have a Zotery style template for Acta Cryst and the like, (s)he
wishes to share? I cannot find it in the repository, but perhaps someone has
made one for private use.
Cheers,
Robbie Joosten
Biochemistry
Netherlands Cancer Institute
used.
Cheers
-- Ian
On Wed, May 4, 2011 at 8:05 AM, Robbie Joosten
robbie_joos...@hotmail.com wrote:
Hi Everyone,
Does anyone have a Zotery style template for Acta Cryst and the like, (s)he
wishes to share? I cannot find it in the repository, but perhaps someone has
made one
: CCP4BB@jiscmail.ac.uk
You can use this
http://www.somwhere.org/csl/
to build your style.
Darren
On 4 May 2011 09:05, Robbie Joosten robbie_joos...@hotmail.com wrote:
Hi Everyone,
Does anyone have a Zotery style template for Acta Cryst and the like, (s)he
wishes to share? I cannot find
Dear Kenneth,
IMO there is no resolution cut-off to decide to go from TLS to individual
anisotropic Bs. I use the number of reflections per atom. You are refining 9
parameters per atom so you need quite a lot. When I have18 ref/atom I switch
to anisotropic. I try both isotropic and anisotropic
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