Perhaps a silly question: will old entries with SPLIT records be superseded by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:
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
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
-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
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
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 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 Joel,
You can just replace your current 'refmac5' and 'libcheck' files. Perhaps after
making a backup. They are in the 'bin' directory of your CCP4 installation.
The easiest way to find them is using 'which refmac5'.
HtH,
Robbie
Verzonden met mijn Windows Phone
Apart from editors we also need tools to validate mmCIF files for integrity,
similar to what W3C has for (x)html and css.
I've mostly dealt with mmCIF reflection files so my experience with what can go
wrong is limited. So far, I encountered these 'issues' that may be flagged.
1) Data items
Hi Omid,
Sometimes the choice of TLS groups and to a lesser extent the initial B-factor
matter a lot. You should try a few other TLS group selections and see if these
give nicer results. Things to try: TLSMD, including or excluding ligands and
carbohydrates, other common-sense or gut-feeling
Dear Monica,
The CCP4 program EDSTATS will give you the number you need, without any hassle.
Give it a try.
Cheers,
Robbie
Sent from my Windows Phone
Van: MONICA MITTAL
Verzonden: 13-8-2013 7:57
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] RSCC
Dear all
I
Hi Shane,
Option one and two may both work. The extra group is not a problem unless it
doesn't actually improve the fit with the data much. If you really have very
little data, you should consider first using one overall residual B-factor
and try to get the most out of the TLS. You can try
.
Cheers,
Robnie
Sent from my Windows Phone
Van: Andrew Leslie
Verzonden: 22-8-2013 10:01
Aan: Robbie Joosten
CC: CCP4BB@JISCMAIL.AC.UK
Onderwerp: Re: [ccp4bb] TLS group assignment near poorly ordered loop
Hi Robbie,
I was interested in a couple
Hi Bernhard,
snip
But the real objective is – where do data stop making an improvement to the
model. The categorical statement that all data is good
is simply not true in practice. It is probably specific to each data set
refinement, and as long as we do not always run paired refinement
Hi Frank and Ian,
We struggled with the small changes in free R-factors when we implementing
the paired refinement for resolution cut-offs in PDB_REDO. It's not just the
lack of a proper test of significance for (weighted) R-factor changes, it's
also a more philosophical problem. When should you
Hi Phil,
When I wrote cif2cif to deal with reflection files from the PDB I opted for
good-enough parsing to provide input for cif2mtz. This was a while ago,
reflection files were still a mess at the time and my programming skills
never tested in practice. I just added support for anything that
Hi Peter,
Thanks for posting the startools, I think many developers can benefit from
these.
[snip]
One final point on this: line-by-line processing needs to allow for the fact
that
there is no requirement at the format specification level for reflection data
to
be one reflection per
Hi Mahesh,
They will be close but not the same. RMSDs should be very close normally,
but different treatment of hetero compounds (ligands and such), outliers and
LINKs added during annotation may cause small deviations. The deviations in
R-factors can be much larger for all sorts of reasons. The
Can the fixes in the CCP4 dictionary be rolled out through the update system
of CCP4? That way we can avoid (at least to some extent) that people keep
working with erroneous restraint files. Some of these errors can really mess
up your structure.
Cheers,
Robbie
-Original Message-
From:
Hi Ed,
WHAT_CHECK checks water that may be ions and also checks the identity of ions
already built. The check my metal server is also very good for final validation
of ions.
Cheers,
Robbie
Sent from my Windows Phone
Van: Edward A. Berry
Verzonden: 9-11-2013
Dear Uma,
These look like waters to me. Generally, for ion detection you can use WASP or
WHAT_CHECK and for validation of built ions you can use the CheckMyMetal server.
Cheers,
Robbie
Sent from my Windows Phone
Van: Uma Ratu
Verzonden: 24-11-2013 1:15
Aan:
Dear all,
We are happy to announce the PDB_REDO web server at
http://xtal.nki.nl/pdb_redo
The
PDB_REDO server refines any structural model you are working on, by
optimising REFMAC refinement and by partial model rebuilding. The
process is fully automated [1] so you only need to provide
Hi Ian,
This probably doesn't affect the MTZ file that comes out of it
but it will affect the statistics of the twinning tests.
I'd be interested to see if this solves the cases where ctruncate goes into an
infinite loop during the twinning tests.
Cheers,
Robbie
Date: Sat, 30 Nov 2013
Dear Faisal,
The PDB_REDO server returns a .pdb file with residual B-factors after TLS,
to submit a model to the PDB it has to have total B-factors. To get those
you can run the CCP4 program TLSANL. The program can read the TLS
information straight from the .pdb file, but if you have an older
Hi Folmer,
Perhaps because of the one year limit of keeping PDB entries in the 'HPUB'
status.
So when a PDB entry is retracted before release, is the PDBid recycled after
a while?
Cheers,
Robbie
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf
of small
molecule chemistry.
Cheers - M
*https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg33403.html
From: Robbie Joosten robbie_joos...@hotmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Saturday, 1 February 2014, 12:48
Subject: Re: [ccp4bb] resubmission of pdb
Hi
Dear Laurent,
1) Refmac mentions gaps explicitly in the LINK records, the PDB does it in a
REMARK record (by comparing the atom records to the sequence of your
crystallised construct). If you just remove the gap-LINKs before deposition
(without adding TER records) it should work.
2) First of
Just to add to Matthew's good advice, UNK is the standard residue name for
unidentified amino acids. Using it for your compound may cause conflicts in
other programs such as COOT.
Cheers,
Robbie
Sent from my Windows Phone
Van: Matthew Franklin
Verzonden:
It's not an e-mail bulletin board, but Researchgate seems to be quite popular
for wet lab questions. IMO the QA section of the social network is a bit
messy. That said, the quality seems to improve gradually.
Cheers,
Robbie
Sent from my Windows Phone
Van: Paul
eleanor.dod...@york.ac.uk
wrote:
I agree with Frank - it keeps crystallographers modest to know how
challenging wet lab stuff still is..
Eleanor
On 12 February 2014 19:23, Robbie Joosten robbie_joos...@hotmail.com
wrote:
It's not an e-mail bulletin board, but Researchgate seems to be quite
Dear Koji,
In addition to all the things Tim said, you may also have a conflict between
the ligand conformation you modelled and the conformation described in your
restraint file. The Refmac logfile will mark any really severe outliers, but
smaller problems can still exist. Try regularising
Hi Louise,
You can go through the mon_lib_list.cif file of the CCP4 dictionary to get a
name that is free (e.g. A97). It would be nice is a certain name would be
reserved for this by the PDB. LIG was a good candidate, but it's gone just
like other nice options (XXX, ZZZ, 000).
Cheers,
Robbie
Dear Jacob,
There are a lot of potential problems with ion validation, that make obtaining
a reliable answer difficult. If you want to datamine ion validation results,
you can use the ready-made WHAT_CHECK files in the PDBREPORT databank for
original PDB files or in the PDB_REDO databank for
Dear Wolfram,
First of all you should make sure you have substantial twinning. Is the twin
fraction close to zero, then don't use a twin target. Is twinning detected by
several test, then there is a good chance your data are twinned.
As for validation, if you do not completely trust your
Hi,
Did you look at the same structure in the PDB_REDO databank
(www.cmbi.ru.nl/pdb_redo)? If the problem can be solved, the structure and maps
should be there. If it cannot, you might get a slightly more informative error
message from the WHY_NOT server.
Cheers,
Robbie
Sent from my Windows
Hi Rob,
Thank you for that cool tool. Such a thing would be nice to have in the CCP4
distribution (hint!).
Cheers,
Robbie
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Robert Oeffner
Sent: Sunday, April 13, 2014 17:11
To:
Dear Peter,
I'm a novice of coot and ccp4. Now I'm doing refinement using both refmac5
and coot.Here are some problems I'm facing. Really hope you can give me
some suggestions.
1、THE RESOLUTION OF THE DATA IS 2.5 angstrom. After first refinement of
refmac5 I got R factor which is 0.26 and R
.asp
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Robbie Joosten
[robbie_joos...@hotmail.com]
Sent: Monday, April 21, 2014 4:40 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] coot problems to decrease R FREE
Dear Peter,
I'm
to the test set. However, this bias is lost
after (converged!) reciprocal-space refinement.
I think that for the final R-free these are equivalent.
Cheers,
Robbie
-Original Message-
From: Pavel Afonine [mailto:pafon...@gmail.com]
Sent: Thursday, April 24, 2014 17:27
To: Robbie Joosten
Hi Pavel,
I agree that you bias R-free after the real-space refinement
well, ok, isn't it enough to realize that this is bad and should be avoided ?
(I
guess we all know we should never bias Rfree!)
My point was that we normally do not calculate R-free after real-
Hi Robert,
This is very easy with the CCP4 program JLigand. Just start a new ligand
with the sulfur atom, add the phenyl groups, the extra bond and the
hydrogens. Then regularise and save the restraint file.
HTH,
Robbie
-Original Message-
From: CCP4 bulletin board
Hi Tim,
PDBe always posts the number of new releases on Facebook (gotta like that). The
recent average is about 175 new entries per week.
Cheers,
Robbie
Sent from my Windows Phone
Van: Tim Gruene
Verzonden: 10-5-2014 22:00
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp:
Dear Felix,
I recently had the same problem. I didn't think TER records were a big deal. I
never had a program that did weird thing because of missing TER records. But
well, orders are orders, so we need TER records for deposition. It would be
nice if all refinement programs would write those.
Hi Faisal,
There are no clearly defined targets for rmsd because it is the rms of
values with different standard deviations. You should use rmsZ instead
(reported by Refmac) because the deviations are on the same scale. For rmsZ,
any value below 1.0 is fine if it gives you the best fit with the
Hi Jacob,
Modeling programs need to take hydrogen bonding into account in their force
fields so they typically have good measures for hydrogen bonds. I personally
use YASARA to get the numbers you want.
This is also what PDB_REDO uses to give you the hydrogen bond energy and the
the number of
Hi Tim,
The problem with missing atoms in ligands is that you cannot use the
coordinates for any follow-up calculation that requires ligand topology (e.g.
restraint generation). That forces you to rely on the annotation of the
compound, for instance at the PDB. That can be quite messy and
Joosten; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Invisible atoms in ligands
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi Robbie,
maybe it is good not to use coordinates for calculations if you cannot
measure the coordinates?
Cheers,
Tim
On 06/13/2014 12:35 PM, Robbie Joosten
Hi Faisal,
It is here: http://wwpdb-validation.wwpdb.org/validservice/
Cheers,
Robbie
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Faisal Tarique
Sent: Saturday, July 19, 2014 14:26
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] validation
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
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 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 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:
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 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
- 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 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,
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
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
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
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
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
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
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 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 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 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 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
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
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
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
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:
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
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
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
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 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 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)
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
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 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
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
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
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
, 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
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
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 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
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