Dear James,
You make a very good point. So far we only discussed the option of removing
alls side chain atoms except for CB. What if only a few side chain atoms are
outside the density? Should we just remove those? If we use the argument that
we should remove the atoms we cannot see, then
Nice one Pavel. PDB_REDO actually runs on these files but it's not pretty. I
updated my stripper program to remove all atoms with occ0.00 instead of 0.00
Cheers,
Robbie
Date: Mon, 4 Apr 2011 07:26:23 -0700
From: pafon...@gmail.com
Subject: Re: [ccp4bb] what to do with disordered side
Hi Jacob,
The PDB header has a record for missing atoms. Coot has an option to find them
and any decent validation software will warn about incomplete residues. There
are PDBREPORT entries for every PDB file with a list of incomplete residues. If
a user makes a very small effort, he doesn't
Hi Ethan,
Awsome progress! Really, I looked for other options like such. 2011
will be a good year for crystallography. I should implement this in PDB_REDO.
Cheers,
Robbie
Date: Thu, 31 Mar 2011 23:06:47 -0700
From: merr...@u.washington.edu
Subject: [ccp4bb] Crystallographic Breakthrough
Hi Frank,
I described in the previous e-mail the probabilistic interpretation of
B-factors. In the case of very high uncertainty = poorly ordered side
chains, I prefer to deposit the conformer representing maximum a
posteriori, even if it does not represent all possible conformations.
detwinning. If you R(-free) is still
considerably lower than the one from the 'regular' refinememt then you are a
lucky guy and the twinned refinement just brought you to a lower minimum.
Cheers,
Robbie Joosten
Date: Thu, 10 Feb 2011 21:36:31 +
From: ga...@ysbl.york.ac.uk
Subject: Re: [ccp4bb
detwinning. If you R(-free) is still
considerably lower than the one from the 'regular' refinememt then you are a
lucky guy and the twinned refinement just brought you to a lower minimum.
Cheers,
Robbie Joosten
Date: Thu, 10 Feb 2011 21:36:31 +
From: ga...@ysbl.york.ac.uk
Subject: Re: [ccp4bb
of hydrogen bonds upon folding is quite useful.
Just don't expect miracles.
Cheers,
Robbie Joosten
Date: Tue, 8 Feb 2011 10:52:09 -0800
From: eid...@blur.compbio.ucsf.edu
Subject: Re: [ccp4bb] quality homology model
To: CCP4BB@JISCMAIL.AC.UK
Hi Susy,
Before going
of hydrogen bonds upon folding is quite useful.
Just don't expect miracles.
Cheers,
Robbie Joosten
Date: Tue, 8 Feb 2011 10:52:09 -0800
From: eid...@blur.compbio.ucsf.edu
Subject: Re: [ccp4bb] quality homology model
To: CCP4BB@JISCMAIL.AC.UK
Hi Susy,
Before going
Dear Careina,
Keep in mind that MolPrrobity does not see symmetry (unlike RefDens or
WHAT_CHECK). This means that the clashes that may come from having the wrong
spacegroup are not detected.
Good luck,
Robbie Joosten
Date: Tue, 18 Jan 2011 10:52:48 +0100
From: mjvanra...@cnb.csic.es
+
From: paul.ems...@bioch.ox.ac.uk
Subject: Re: [ccp4bb] Mg2+ or water
To: CCP4BB@JISCMAIL.AC.UK
On 20/12/10 21:48, Robbie Joosten wrote:
Also note that Mg2+ is significantly smaller than water. It fits in
places where water cannot go. This doesn't look like a magnesium site
Dear Hailiang,
I regularly separate TLS refinement from restraint refinement to spead things
up when I try to optimise the restraint weights. Using Refmac 5.6, I do the
following:
- Do TLS Refinement in refmac
- Use TLSanl to change the total B-factors to residual B-factors.
- Load the output
diagram of a tripeptide with 'R1', 'R2'
and 'R3' at the side chain positions). Do any of you know nicer examples
(preferably with episode title/number)?
Best wishes,
Robbie Joosten
position in the file (otherwise real-space refinement won't work).
You probably also need to make LINK records, which you can copy from an
existing PDB file (1xer has the links you need).
Helix-Turn-Helix,
Robbie Joosten
Date: Thu, 4 Nov 2010 09:04:53 -0400
Hi Bart,
I agree with the building strategy you propose, but at some point it stops
helping and a bit more attention to detail is needed. Reciprocal space
refinement doesn't seem to do the fine details. It always surprises me how much
atoms still move when you real-space refine a refined
Hi Phil,
I do, but the freeR flag problem is easily circumvented. One can just use cad
with the output mtz from ctruncate and the input mtz:
cad \
HKLIN2 $WORKDIR/raw.mtz \
HKLIN1 $WORKDIR/ctruncate.mtz \
HKLOUT $WORKDIR/ctruncate_withRfree.mtz \
eof $WORKDIR/mtz_creation.log
LABIN FILE 2
is not complete. I may also have overstated some of the
rules to get the discussion going. Any addidtions are welcome.
Cheers,
Robbie Joosten
Netherlands Cancer Institute
Apologies if I have missed a recent relevant thread, but are lists of
rules of thumb for model building and refinement?
Anthony
of them seem to be fairly new
(pdbids 3[a-n]??).
I agree that Jackie should build the whole molecule to make sure all restraints
kick in. It's only a little extra work to set the occupancy correctly for all
atoms. In Coot one can do that with the 'residue info' option.
Cheers,
Robbie Joosten
or not. I'm guessing it's a HIS so the C11
atom should be a hydrogen bond donor or acceptor. The Residue next to the HIS
(ASP or ASN) may tell you more about the protonation of the HIS. This is a fun
game.
Cheers,
Robbie Joosten
Date: Fri, 1 Oct 2010 17:21:31
Dear Petr,
I agree with Tom that there is no need to release the NCS in the final rounds
of refinement. You just end up throwing away good work. Perhaps you can tweak
the NCS a bit to try to get better results (even though your current results
sound fine). It's difficult to set up the right
Dear Rex,
Beta-lactose is in Ligand-Expo as 'LAT' so I'd stick with that.
Regards,
Robbie
Date: Tue, 17 Aug 2010 22:58:27 +0100
From: rex.pal...@btinternet.com
Subject: [ccp4bb] Lactose again
To: CCP4BB@JISCMAIL.AC.UK
In Refmac: Does anyone know if lactose should be
designated as one
at the electron density maps
generated by the EDS (http://eds.bmc.uu.se/eds/) or PDB_REDO
(http://www.cmbi.ru.nl/pdb_redo).
HTH,
Robbie Joosten
Date: Tue, 13 Jul 2010 18:10:37 +0530
From: m.pran...@gmail.com
Subject: [ccp4bb] Judging a PDB
To: CCP4BB
It means that the CMBI's server migration is still ongoing. The problem should
be temporary.
Cheers,
Robbie
Date: Tue, 13 Jul 2010 13:03:05 -0700
From: xtald...@gmail.com
Subject: Re: [ccp4bb] Judging a PDB
To: CCP4BB@JISCMAIL.AC.UK
On Jul 13, 2010, at 5:49 AM, Robbie Joosten wrote
of a percent(age point).
Cheers,
Robbie Joosten
Date: Tue, 2 Mar 2010 08:44:18 -0800
From: merr...@u.washington.edu
Subject: Re: [ccp4bb] Deposition of a BUSTER refined structure
To: CCP4BB@JISCMAIL.AC.UK
On Tuesday 02 March 2010 07:09:47 Melanie Vollmar wrote
a 'REMARK 280' to your PDB file it makes
checks a bit more reliable. At any rate you should check the suggestions
carefully by hand. At high resolution one tends to get alternate waters which
really messes up things.
Cheers,
Robbie Joosten
Date: Mon, 15 Feb
Dear James,
When reading and writing SEGIDs, why bother making it case unsensitive? Most
programming/scripting languages read text case sensitive anyway. Assuming
people don't type SEGIDs by hand, differences in capitalization may be
significant.
When you are generating SEGIDs from
Hi Fred,
PS And what I find really annoying is the atom type specified in columns
77-78, since the information is already present in the same line, as
CA, N, HG etc. Sometimes I just forget to check what's present in
these 2 columns and I have problems with some programs that refuse to run.
Dear CCP4BB-ers,
The official DSSP is now also available for Intel Macs:
http://swift.cmbi.ru.nl/gv/dssp/
We have limited access to Mac computers, so the software is not as thoroughly
tested as the Linux and Windows versions. Feel free to send bug reports.
Best wishes,
Gert Vriend Robbie
. There has already been a lot of
improvement in that field lately, so I'm sure we'll get there.
Best wishes,
Robbie Joosten
Best regards,
Herman
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Damian Ekiert
Sent: Wednesday, December 23, 2009
requirements.
PDB-care and CARP are both very usefull. Unfortunately, the service is
currently down (http://www.dkfz.de/spec/glycosciences.de). Just make sure
the links between your carbs are correct and, please, remove the O1 atoms
when needed ;)
Cheers,
Robbie Joosten
Dear Nicholas,
Yes we are diverging, but you make a few important and valid points. So
let's diverge some more...
I fully agree that validation tools should not tell people how to do
science. That would kill free thought and lead to circularity in the
results. A typical example is the question
Dear Fred,
People have already done this for all PDB entries:
- http://eds.bmc.uu.se/eds/ : maps and many crystallographic stats
- http://www.cmbi.ru.nl/pdb_redo : maps and re-refinement. And yes, the
stats and maps do improve most of the time, unfortunately also for
structures that are not
Dear Eric Bennett,
3g6a was processed by PDB_REDO (without the original R-free set which
sadly wasn't deposited) on Monday, 20 July 2009 at 21:35 CEST with
PDB_REDO version 2.6: http://www.cmbi.ru.nl/pdb_redo/g6/3g6a/index.html
That was roughly two months after the last revision (the entry is
would spend a week per year
getting/keeping kids excited about science, we really wouldn't need a TV
channel to grasp their attention.
My n cents.
Cheers,
Robbie Joosten
; D54:547-557
HTH,
Robbie Joosten
Netherlands Cancer Institute
Amsterdam, The Netherlands
Date: Wed, 23 Sep 2009 22:37:17 -0700
From: det...@uoxray.uoregon.edu
Subject: Re: [ccp4bb] Rfree in similar data set
To: CCP4BB@JISCMAIL.AC.UK
Yes
Dale Tronrud
Hi Engin,
The latest version of the Refmac dictionary has the correct geometry (and
loads of other improvements). You can download it here:
http://www.ysbl.york.ac.uk/~garib/refmac/latest_refmac.html
Cheers,
Robbie Joosten
Hi everyone,
We just realized in the lab that the dimethyl-lysine
have known that there was something wrong
with them.
Cheers,
Robbie Joosten
, an empty set
(http://www.cmbi.ru.nl/WHY_NOT/comments_withcomment.action?scomid=10)
Cheers,
Robbie Joosten
Centre for Molecular an Biomolecular Informatics
Nijmegen, the Netherlands
Well, either there haven't been any replies yet or my institution's
email server is unhappy with me (if it's email
.
Cheers,
Robbie Joosten
From: Winn, MD (Martyn) [EMAIL PROTECTED]
Sent: Saturday, March 29, 2008 20:57
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [phenixbb] Rant: B vs TLS, anisou, and PDB headers
2) All you need to reproduce the R-factors are the ATOM records and
structure factor formula
, insanely
high B-factors, or are too far away from the other atoms to make hydrogen
bonds.
To get reasonable numebers you'll have to re-evaluate a numebr of PDB
entries.
Best wishes,
Robbie Joosten
Center for Molecular and Biomolecular Informatics
Nijmegen, The Netherlands
Hello everyone,
I would
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