Dear colleagues,
I would like to draw your attention to a notification from the wwPDB partners
about Deposition and Release of PDB Entries Containing Large Structures -
see:
http://www.wwpdb.org/news/news_2013.html#22-May-2013
There are major changes afoot in the way large
Wait, so a geometer measures ges, an odometer measures ods, and a kilometer
measures kils?
--dvd
On Thu, 20 Jun 2013, Tim Gruene wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Ed,
to me, an '-ometer' is a device that measures whatever you put in
front of the 'o', so in case of
is hyphenated kilo-meter, no kil-ometer, so the origin
of that word is nothing to do with 'ometer'. Remembering stuff from
your school days help a great deal understanding the world around you ;-)
Best,
Tim
On 06/20/2013 01:14 AM, Gerard DVD Kleywegt wrote:
Wait, so a geometer measures ges
As for Gerard's follow up, I remind him of the immortal wisdom of Jack
Handey:
Maybe in order to understand mankind, we have to look at the word itself.
Basically, it's made up of two separate words ? mank and ind. What do
these words mean? It's a mystery, and that's why so is mankind.
wwPDB Workshop on mmCIF/PDBx for Programmers
What, why and how?
--
The world of the PDB will be changing rapidly and profoundly over the next few
years. A major change will involve the transition from PDB to mmCIF/PDBx as
the
On Thu, 22 Aug 2013, Gloria Borgstahl wrote:
We have a protein sequence that probably contains OB folds. What is the
best way to search for the top structural homologs to this sequence in the
pdb? G
Hi Gloria,
If you expect decent sequence simnilarity to one or more proteins in the PDB,
Dear all,
At present, unmerged data cannot be handled properly as part of a PDB
deposition. One reason for this is that changes to the mmCIF/PDBx data model
will be required (at the moment, hkl must be unique within the reflection
data, which is logical for merged data but precludes handling
it.
It is strange to hear on a discussion board that recently considered the
advantages of depositing complete image data, that a case will have to
be made for allowing the deposition of full unmerged datasets.
++Martyn
On 16/09/2013 14:03, Gerard DVD Kleywegt wrote:
Dear all,
At present
The server has been rebooted and appears to be working again.
--Gerard
On Fri, 25 Oct 2013, Rojan Shrestha wrote:
Hello,
Is EDS (electron density server) dead? In the absence of EDS, how can be mtz
file directly downloaded?
Regards,
Rojan
Best wishes,
--Gerard
Dear colleagues,
The wwPDB partners are pleased to announce that X-ray structure validation
reports can now be generated on demand by macromolecular crystallographers by
using the new stand-alone wwPDB validation server.
For the full scoop, see:
Hi all,
You may not have noticed, but 19 March 2014 was VR Day - the day that new
style wwPDB validation reports for all X-ray structures were made publicly
available - see http://www.wwpdb.org/news/news_2014.html#18-March-2014
The validation-related files for individual X-ray PDB entries
, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ ,
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18
De : Gerard DVD Kleywegt ger...@xray.bmc.uu.se
? : CCP4BB@JISCMAIL.AC.UK
Envoy? le : Mercredi 16
Hi all,
You may not have noticed, but 19 March 2014 was VR Day - the day that new
style wwPDB validation reports for all X-ray structures were made publicly
available - see
Hi all,
You may not have noticed, but 19 March 2014 was VR Day - the day that new
style wwPDB validation reports for all X-ray structures were made publicly
available - see
Hi all,
You may not have noticed, but 19 March 2014 was VR Day - the day that new
style wwPDB validation reports for all X-ray structures were made publicly
available - see
Hi all,
You may not have noticed, but 19 March 2014 was VR Day - the day that new
style wwPDB validation reports for all X-ray structures were made publicly
available - see
Hi all,
I don't know why my posting about validation reports re-appeared several
times. The mail headers show that all 4 came through the domain ouhsc.edu but
why they would be resent to ccp4bb is not clear, nor why this only happened
with my posting.
--Gerard
See: http://www.wwpdb.org/news/news_2014.html#06-May-2014
Even if you don't deposit anything, we'll reach the 100,000-entry milestone
with next Wednesday's release :-)
--Gerard
On Fri, 9 May 2014, mesters wrote:
Great, just a few more structures to deposit and then 100.000 structures to
:33 PM, Gerard DVD Kleywegt wrote:
See: http://www.wwpdb.org/news/news_2014.html#06-May-2014
Even if you don't deposit anything, we'll reach the 100,000-entry
milestone with next Wednesday's release :-)
--Gerard
On Fri, 9 May 2014, mesters wrote:
Great, just a few more structures to deposit
MAPMAN contains several related options, e.g. CEll, SPacegroup, TRanslate and
GTranslate, PAste (see the manual for caveats -
http://xray.bmc.uu.se/usf/mapman_man.html ). Saving as an ASCII file and
editing may also work, if you know what you are doing.
--Gerard
On Tue, 20 May 2014,
What you want is a test for how well each model agrees with its own map. It
is fair to argue that the model that is more self-consistent (agrees better
with its own map) is the better model. But you won't learn that by
comparing model A to map B.
However, conversely, if your modified model
Dear all,
The EMDB team at the Protein Data Bank in Europe (PDBe; http://pdbe.org) has
two vacancies for scientific programmers to work on an exciting new MRC and
BBSRC funded project to help bridge the worlds of cellular and molecular
structural biology. The project aims to develop:
1) a
[Cross-posted from the 3DEM mailing list.]
--Gerard
-- Forwarded message --
Date: Wed, 4 Apr 2012 16:34:39 +0100
From: Helen Saibil h.sai...@mail.cryst.bbk.ac.uk
To: 3DEM Mailing List 3...@ncmir.ucsd.edu
Subject: [3dem] CCP-EM positions now available
Dear Colleagues,
We have
Are you an aspiring science communicator who has a wonderful way with words?
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is looking for an
enthusiastic 'jack of all trades', to coordinate its outreach activities. We
are looking for someone who will raise the profile of PDBe through
Hi Paul,
You saw the wwPDB/CCDC JPG in my PPT at GSK :-)
Yes, wwPDB and CCDC have signed an MoU. In pounds and pennies it means,
amongst a number of other things, that wwPDB will be allowed to use Mogul in
its validation pipeline and that wwPDB will be allowed to incorporate and
redistribute
A good tool should leave b as is: it is ASX (the standard ambiguity
code for ASP or ASN). j, o and u are a different matter :-)
http://www.uniprot.org/manual/non_std
Selenocyteine [sic!] and pyrrolysine are represented in the sequence using
the one-letter codes U for selenocysteine and O for
Hi all,
E3 ubiquitin ligase is responsible for flagging proteins for degradation by
transferring ubiquitin from a donor protein onto the molecule to be degraded.
It is activated by phosphorylation of a tyrosine which promotes a huge
conformational change, swinging its RING domain 180 degrees
Hi all,
In the past couple of years, Mark Harris in Uppsala has developed a bunch of
programs and servers that are useful for crystallographers, structural
biologists and structural bioinformaticians. Some of his programs are listed
here:
http://xray.bmc.uu.se/markh/programs.html
Because I want all the structures of a particular protein itself, not it's
homologues. I just went through several cycles of reducing E-value down to
If you know the UniProt accession code of your protein, then UniPDB is your
friend - pdbe.org/unipdb
If not, try pdbe.org/fasta where you can
Hi all,
Plants suffer from DNA damage caused by ultraviolet light in the same way that
humans do. Unlike us though, they cant put on a sunhat (or move to England) to
avoid the suns rays. Read more about how plants sense UV-B light and turn on a
suite of genes to protect their DNA against its
Hi all,
Twice a year, the Protein Data Bank in Europe (PDBe; http://pdbe.org) releases
new, improved and updated versions of its tools and resources. Below is a
brief description of new features and services that have been released this
summer (or what passes as summer in the UK). As always,
Dear all,
The EDS server was unfortunately down for a number of days. However, as of
yesterday it is up and running again. Apologies for the inconvenience.
http://eds.bmc.uu.se/
--Gerard
**
Hi all,
The Protein Data Bank in Europe (PDBe; pdbe.org) is looking to recruit an
expert structural biologist to join the PDBe curation team at the EBI near
Cambridge, UK. Applicants should be computer-literate and possess a recent PhD
in some area of structural biology or structural
This sounds like a job for SPASM. We used it to find instances of left-handed
helices in the PDB. See:
- SPASM: http://www.ncbi.nlm.nih.gov/pubmed/9917419
- Left-handed helices: http://www.ncbi.nlm.nih.gov/pubmed/15740737
The database for SPASM hasn't been updated for a few years, but it may
If you have an old copy of MOLEMAN (not MOLEMAN2!) lying around, this can be
done very easily (ever since it was programmed on Valentine's Day 1993, in
fact - I even remember who my Valentine was :-) - see:
http://xray.bmc.uu.se/usf/moleman_man.html#S13
- READ your original model (PDB
Hi all,
The Protein Data Bank in Europe (PDBe; pdbe.org) is looking to recruit a
junior structural biologist to join the PDBe curation team at the EBI near
Cambridge, UK. Applicants should be computer-literate and possess a recent PhD
in some area of structural biology or structural chemistry
I am refining a lectin-carbohydrate complex. The electron density clearly
shows that a mixture of alpha- and beta-anomers of the sugar have bound in
the crystal. How can i generate appropriate restraints for the carbohydrate
with alternative conformations (i.e. alpha- and beta-anomer)? At the
hahaha! brazilian humour - always cracks me up!
for those of you whose portuguese is a bit rusty, let me provide a quick and
dirty translation:
video de pessoas famosas em cada situa?ao!!!
videos of famous pessaries in situation comedy
clika o lik p/ ver o video se nao der disite a
gruzi dirk,
come on - lighten up a little! your reply wasn't funny or helpful either -
just moralising. (by the way - 't is a strange fact that whenever i get any
negative reactions to my own postings they stem *exclusively* from any or all
of these three countries: the us, germany and
Risking a potentially trivial question:
Is there a program that will calculate the RMS of distances
between specified (listed) atoms in two different structures?
As far as I could see, LSQMAN will only compute same with same?
lsqman does in fact calculate rmsd valus between arbitrary sets of
Dear structural(-ly interested) biologist !
HIC-Up, the Hetero-compound Information Centre - Uppsala, has been updated and
now contains information on 7,452 hetero-entities. This is the last HIC-Up
version prior to the release of the remediated PDB. Hopefully, the remediation
will improve the
Does anybody know, please, any alternative program or trick to transfom the
side chain of a residues into its mutated counterpart, please, with a nice
and smooth visual effect? Does LSQMAN, for example, sort this problem out?
It is not clear to me reading the manual.
no, it won't. however, in
What about to do a cartesian morphing with the mutated residue
added (or removed) atoms having initial ( or final) coordinates taken from
previous common atom?
Will work? Coloring may be a factor... but with a manual editing
perhaps...
you mean, for instance, if you
I thought that I would never have to disagree with both Eleanor and
Tassos in the same email, let alone risk being burnt at a stake as a
heretic for doubting the Gospel according to Kleywegt, but in my
but ... but ... i haven't even said anything! i'm innocent! my name is being
used in vain!
We have crystallized a cyanobacterial phycoerythrin which having two (alpha
subunit) in an assymetric unit and held together by only three hydrogen bonds.
When we compare the A and B molecule the RMSD is 1.32. because they same
sequences then how it is possible to that two molecules are
Can you explain the define of the bond length and bond angel--especially
bond angel--here?
i leave the definition of angels (be they ideal or not) to clerics, but if you
want to find out about bonds and angles, AND YOUR SUPERVISOR IS REALLY UNABLE
OR TOO BUSY TO EXPLAIN THESE BASIC
them today before I post my mail, but unable to access them. For some
reason, wiki is forbiddon here. I really coouldnot find the best answer and
have discussed
i am shocked. i just checked with one of my 25 chinese students here and
indeed even universities in china do not have access to a
Please do NOT use the BB for abuse.
thank you for your support. although i think some abuse of the english
language is unavoidable in an international forum like this
--gerard
(more important issue: http://www.irrepressible.info/)
hi,
I am writing a PERL script to execute a number of CCP4 commands (ncsmask,
pdbset, and dm) in succession. I have tried using system call or PIPE
command, neither of which work. The ccp4 scripts generated work
independently on the command line.
we do this in the eds map generation
ni hao,
I have a question about how to improve the electron density. I have two
indepedent molecules in the asymmetric unit (1.9 A resolution). I solved the
structure with PHASER and refined with CCP4i (Rfree = 0.29).
For the first molecule, the density is very good, but for the second
manipulate some sequences into various forms, and I was imagining a moleman
homolog for bioinformatics (perhaps seqman?).
as a matter of fact, i did write exactly that program nine years ago -
http://xray.bmc.uu.se/usf/seqman_man.html :-) - not quite a 'ccp4 for
bioinformatics' but indeed
I'm looking for a convenient way of converting a .cif structure factor file
(from PDB) to a map-file (e.g. .mtz) to open with COOT for example..?
Already tried ccp4i with 'Convert to/modify/extend MTZ', but got a bunch of
errors when opening with coot..
doesn't coot have an 'import from EDS'
not sure if this announcement has made it to ccp4bb yet ...
--bruce
-- Forwarded message --
Preliminary announcement for the
2008 Kyoto Crystallographic Computing School
Sharing our knowledge
August 18-23, 2008
Kansai Seminar House,
Forwarded on behalf of Lachlan Cranswick.
--dvd
-- Forwarded message --
2008 Kyoto IUCr Crystallographic Computing School - Sharing our knowledge
(preliminary announcement)
Kyoto Crystallographic Computing School
Kansai Seminar House,
One small step for a crystallographer, one giant leap for mankind! (*)
--
For those of you who didn't see it, the following was posted to the PDB
mailing list last week:
Announcement: Experimental Data Will Be Required for
Terese Bergfors will be organising her famous Uppsala University Practical
Protein Crystallization Course again, from 15-19 September, 2008. For more
information, see the course website at:
http://xray.bmc.uu.se/terese/course/course.htm
--dvd
Dear structural(-ly interested) biologist !
HIC-Up, the Hetero-compound Information Centre - Uppsala, has been updated and
now contains information on 7,870 hetero-entities. This is the first HIC-Up
version after the release of the remediated PDB. A few changes had to be made
to the
Dear James!
Initially I was shocked by the profound implications of your discovery! I
immmediately phoned my good friend, Sen. John McCain, to discuss the issue. As
you know, Sen. McCain was an aspiring physicist back in the 1920s, when he was
in his forties. He pointed me to a little known
I have a sequence that I would like to model by threading onto each
subunit of a homo-tetramer of a related protein (crystal structure). It
doesn't work to thread each subunit individually and then 'recombine' the
homodimer as a single PDB because the interfaces suffer from clashes and
I am currently refining a high-resolution structure that has many reflections
(~180,000). I
would like to halve the R-free set from 5% to 2.5%, and am unsure how to do so.
Any advice
will be greatly appreciated.
there is a bunch of commands in dataman to do this (and other things) to your
I am trying to make a quite classic demonstration of electron density map
sliced and contoured as (smoothed) isoheight curves. The sliced section is
random and NOT along any main cell axes. I am curious if there is any
crystallographic software can handle this, which will save me from writing
RE: [ccp4bb] Facebook for NeerdsIf you would fourier transform the whole
site, you could get myspace back, but where would you get the phases?
errrm, phasebook?
--dvd
**
Gerard J. Kleywegt
[Research
Many of the positions advertised on CCP4 (and elsewhere) are also copied to
the 'Job openings' page of the Swedish Structural Biology Network (SBNet;
http://xray.bmc.uu.se/sbnet/) by Henrik Hansson (Uppsala):
http://xray.bmc.uu.se/sbnet/positions.html
Note that this page also
I suspect everyone is refering to Rost's twilight zone in sequence
similarity where homology modeling trials had better be avoided.
If so, the twilight zone would rather correspond to any indefinite
or transitional condition(s) with no applicable or ever relevant binary
constraint(s).
actually,
But how do we establish phylogeny? - Based on simple similarity!
ah! the old rhetorical trick of changing the problem or question a posteriori!
all i pointed out was that things can't be 25% homologous (well, i can think
of a contrived example in which two four-domain proteins have one
a few öre's worth from sweden ...
there is a surprising number of deposited ligand structures where
re-refinement shows that the ligand is built into noise.
nope, not surprised at all:
- http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=89
-
issue. Could I just confirm whether or not you think its necessary to
transfer initial free R assignment to any new data sets or to isomorphous
data sets such as substrate complexes.
well, i would always do a slow-cool at the start so then it would not be
necessary to transfer them
ian
As suggested by Tassos, what we need now more than ever is some Dutch
diplomacy so that he healing can really begin. Various people have argued for
a shorter term (Brazilians, Pflugrath) and since I'm personally rather partial
to Brazilians I would say we ought to go with that and shave off a
Can someone tell me if there is a relatively straightforward way of
transferring Free R flags between two CNS format reflection files ?
DATAMAN - http://xray.bmc.uu.se/usf/dataman_man.html#S63
--dvd
**
Are there any good free programs for the design of one's own sparse matrix
screens? I am looking for something in the lines of a set of mixtures of
what gives you the best coverage of, say, seven variables with five states
each in 96 experiments.
If memory serves, both Stefan Knight
leela shetty wants you to join Yaari!
Is leela your friend?
Please respond or leela may think you said no :(
This being Valentine's Day and all, am I the only one who is wondering if
Leela and CCP4BB hit it off?
--dvd
**
I even made the cover! And I hope that (after looking at the cover) all you
BBers will forgive me just this once as this was clearly a once-in-a-lifetime
opportunity. Or, at least, I HOPE only once.
Congratulations, James. But surely you could have found a better example of
medical imaging?
Only problem: it's in Bavaria... and we belive that you will need an
excellent command of the German language both written and spoken to work
here efficiently and live here happily.
Dear das Doktor von Hannes!
Ich das Jobb very interessiert ist worden worden geworden. Die Bayern
placement
The Protein Data Bank in Europe has *three* openings for software engineers or
scientific programmers (one-year contracts):
(1) The PDBe Team has an opening for a software engineer or scientific
programmer to work in the NMR (Nuclear Magnetic Resonance) project. The post
holder will work with
PDBe launches its redesigned website (pdbe.org)
---
The Protein Data Bank in Europe (PDBe; http://pdbe.org) has launched its
redesigned website with lots of new features, enhancements and improvements.
This so-called Midsummer Make-over is the first
The Protein Data Bank in Europe (PDBe; pdbe.org) has a vacancy for the Project
Leader Electron Microscopy position.
For more information:
http://www.embl.de/aboutus/jobs/jobs_embl_ebi_hinxton/2010/w_10_059_ebi/index.html
PDBe is the founder of the worldwide archive of 3D cryo-EM data, the
Traditionally, the Protein Data Bank (PDB) has been accessed mostly by PDB
accession code, or by searches based on information regarding, for instance, a
publication, a molecule name, a sequence or a related 3D structure. While
these methods are valuable for locating a specific PDB entry or
Ni hao,
(1) Will re m2 msk.mask ccp4 instead of re m2 msk.mask mask affect the
results?
Well, that depends entirely on what's in the file! The last parameter is your
way of telling the program what the format of the file is. Mask means one of
the MAMA-supported mask formats - ccp4 means a
I am sorry, I have a very basic quarry regarding the PDB structures. How one
can judge the quality of a deposited PDB data set? Suppose,for e.g., two
PDB's have same R-values and have determined at same resolutions with same
completeness.
You may want to work your way through this tutorial:
If you were born before the Dutch lost their first World Cup final, you may
remember the days when everybody knew that PDB entry 1tim was the structure
of chicken triosephosphate isomerase, 1hhb was human haemoglobin, 1lyz was hen
egg-white lysozyme, etc. Unfortunately, life for a structural
http://pdbe.org/pdbprints
Good idea.
But the icons for published/unpublished, protein present/protein absent,
nucleotide present/nucleotide absent and ligand present/ligand absent look
identical to me - I have to read the alt text.
Is there some colour thing going on here
We are pleased to announce the 2010 Cryo-EM Modeling challenge and a PSB 2011
workshop, organized by Steven Ludtke, Wah Chiu, Helen Berman and Gerard
Kleywegt.
http://ncmi.bcm.edu/challenge
* Modeling as a tool for interpretation of cryo-EM reconstructions *
Cryo-EM
://pdbe.org/advancedsearch?text=lac+repressor
If you want to read more about PDBprints, surf to: http://pdbe.org/pdbprints
Thanks for your feedback!
--Gerard
On Thu, 15 Jul 2010, Gerard DVD Kleywegt wrote:
If you were born before the Dutch lost their first World Cup final, you may
remember
Introducing one-click access to PDB data at PDBe
When you visit the newly redesigned home page of the Protein Data Bank in
Europe (PDBe; http://pdbe.org/), the panel in the centre of your screen
(labelled Home) provides one-click access to PDB
There is an EMBL Interdisciplinary Post-doc (EIPOD) position available to
work on the validation of low-resolution structural models obtained from
small-angle X-ray scattering (SAXS). The project is a collaboration between
EMBL Hamburg (Svergun), EMBL Heidelberg (Gavin) and the EBI (Kleywegt),
As part of the recent Midsummer Make-over of the Protein Data Bank in Europe
website (PDBe; http://pdbe.org/), we introduced a new Wizard tool. The purpose
of the Wizard is to help novice users find stuff on the site, be it one or
more PDB or EMDB entries or information about PDBe tools,
As part of the recent Midsummer Make-over of the Protein Data Bank in Europe
(PDBe) website, we acquired the domain name pdbe.org and have used it to
implement a number of shortcuts to many of our services etc.
- http://pdbe.org/ - the new PDBe website
- http://pdbe.org/1cbs - go directly to
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) offers a number of
educational resources as part of its wider mandate for outreach and training
within the European Bioinformatics Institute (EBI; http://www.ebi.ac.uk/).
As part of this commitment, we offer the PDBe roadshow
There are three more vacancies coming up at the Protein Data Bank in Europe
(PDBe; pdbe.org):
- Head of PDBe Deposition and Annotation
http://ig14.i-grasp.com/fe/tpl_embl01.asp?s=MbkMjPUrEcTFkHhTczjobid=40182,2388233441
- 50% Oracle DBA/50% Senior Software Engineer
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is pleased to
announce the availability of PISA assembly files, summaries and associated XML
descriptors for all relevant entries in the Protein Data Bank (PDB) archive
for download and in-house analysis.
PDBePISA
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is pleased to
announce the Structure Integration with Function, Taxonomy and Sequence
(SIFTS) initiative, a close collaboration between PDBe and UniProt, that aims
to improve the integration of the structural database and other
Dear colleagues,
The EBI is carrying out a user survey about its services, collecting input
from current and potential users. The survey lives here:
http://www.surveymonkey.com/s/EMBL-EBI
- It should take 10-15 minutes.
- There are no compulsory questions.
- You can be
Hi Ian,
First, constraints are just a special case of restraints in the limit
of infinite weights, in fact one way of getting constraints is simply
to use restraints with very large weights (though not too large that
you get rounding problems). These 'pseudo-constraints' will be
For an older paper with several examples, see: Acta Cryst. (1993). D49,
505-512 [ doi:10.1107/S0907444993003737 ], Orientation of non-crystallographic
symmetry axes in protein crystals, X. Wang and J. Janin
My favourite example is 1cel: pdbe.org/1cel and pdbe.org/download/1cel (see:
Following feedback from students, collaborators and other structural
biologists, the Protein Data Bank in Europe (PDBe; pdbe.org) has become aware
of a need for a social networking presence to strengthen the link with current
and potential users of its resources.
So if you would like to
Hi all,
We have two new openings at the Protein Data Bank in Europe (http://pdbe.org -
part of the European Bioinformatics Institute in Cambridge, UK) to work in the
Databases Services team:
- Software/Database Engineer
Not sure if this helps, but MAPMAN contains options to make 1D and 2D
projections - see http://xray.bmc.uu.se/usf/mapman_man.html#S45
Many moons ago, I also wrote a script to generate general projections (e.g.,
onto the plane of an aromatic ring) using various USF programs - you may want
to
This was one of the things that Indonesia was written for (a long time ago, in
a galaxy far, far away), although I'm not sure if it will still run. If you're
desperate, see http://xray.bmc.uu.se/~dennis/
--Gerard
On Fri, 26 Nov 2010, Muhammed bashir Khan wrote:
Dear All;
I have
If you have LSQMAN, this is trivial - read your superimposed files and use the
RMsd_calc command - http://xray.bmc.uu.se/usf/lsqman_man.html#S59
--Gerard
On Tue, 23 Nov 2010, Huiying Li wrote:
Another question on RMSD:
I have two structures of the same protein superposed with the LSQ
Hi all,
This is to inform PDB/EMDB depositors (at PDBe only) and users of PDBe
services (http://pdbe.org/) that we will be operating with a reduced level of
service in the next few weeks:
- on 23 and 24 December we are operating with a skeleton crew, especially in
the depositon and
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