x27;unbiased' way?
> > thanks for your suggestions,
> > Stephen Cusack
> >
>
--
***
* *
* Dr. Martyn Winn
ror message
> child process exited abnormally
> ***
>
>
> #CCP4I TERMINATION STATUS 0 "child process exited ab
ur reseach supervisor or other person who may be
consulted if necessary. All this information will be treated confidentially.
Participants are encouraged to bring their own data.
Martyn Winn
Isabel Uson
Garib Murshudov
es. This is the get-out method if cif2mtz fails. Edit the item
>name to something that is recognised.
Cheers
Martyn
--
***
* *
* D
r research
supervisor or other person who may be consulted if necessary. All this
information will be treated confidentially. Participants are encouraged
to bring their own data.
Martyn Winn
Isabel Uson
Garib
t; > Regards
> > John
> >
> > Dr John W. Liebeschuetz
> > Research & Applications Manager
> > Cambridge Crystallographic Data Centre
> > 12 Union Rd., Cambrid
ers
Martyn
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk
to getting a reply from you on how to
> solve the problem.
>
> Cheers,
>
> Dialing
>
>
>
>
>
--
******
n status 0 "child process excited anormally".
>
> I am looking forward to getting a reply from you on how to
> solve the problem.
>
> Cheers,
>
> Dialing
>
>
>
&g
y (i.e. stereochemically correct)
> > model.
> > >>
> > >
> > > and here are the results of more or less systematic test that
> > prove this:
> > >
> > > see "On contribution of hydrogen atoms to X-ray scattering"
> >
and IRC50666. Further
information is available there. Informal enquiries may be made to Martyn Winn
(martyn.winn at stfc.ac.uk).
Best wishes,
Martyn Winn, Richard Henderson, Alan Roseman, Peter Rosenthal, Helen Saibil and
Ardan Patwardhan
Certainly different programs and different scoring matrices will give different
answers. There is not necessarily a correct answer either, just different
educated guesses. With high sequence identity, the answers should be fairly
consistent. As you reduce the sequence identity (i.e. as it gets m
Reflection cif files from the PDB do not always have cell and symmetry
information in them, particularly the older ones, and it sounds like this is
your case.
In that case, you need to manually copy the cell information from the PDB web
page into the ccp4i interface before running.
HTH
Martyn
But that's not what Paul said. I am sure we all agree the information _should_
be there, but I took Paul to mean that it _is_ there.
If I look at PDBe for 2gs7, go to Downloads and Structure Factors, then the
cell and symmetry is _not_ there.
If I go to RCSB, and click on Structure Factors on th
rer
> and Head of Research Computing,
> Wellcome Trust Centre for Human Genetics,
> Roosevelt Drive, Oxford OX3 7BN, UK
>
> Emails: rob...@strubi.ox.ac.uk Tel: (+44) - 1865 - 287783
> and rob...@esnouf.comFax: (+44) - 1865 - 287547
X flagging
> > > > convention is "1" for working and "-1" for test. So I manually tagged
> > > > the working set with "1" using vi:
> > > >
> > >
Sc.
> > 215 UCB
> > University of Colorado at Boulder
> >
> > gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
> >
> > 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
>
--
***
Forwarded on behalf of Alan Roseman [mailto:alan.rose...@manchester.ac.uk] so
please contact him not me.
Happy New Year to all,
Martyn
Software Developer/ Scientific Computer Progra
Regards,
> >
> > Rojan
> >
> > --
> > This message has been scanned for viruses and
> > dangerous content by MailScanner, and is
> > bel
tlsextract in the CCP4 suite (from Jay Painter and Ethan Merritt).
Martyn
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jochen
Kuper
Sent: 03 February 2011 08:33
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] TLS from PDB records
Dear All,
sorry for the probably silly que
like a simple thing someone would want to do.
>
>
> Thanks,
>
>
> Graeme
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Lab
oops, I did that ... and I'd forgotten all about it ... simpler option than
pointless
m
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> James Holton
> Sent: 18 March 2011 15:49
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Data file wra
I agree there are probably much better and simpler ways of doing this.
But to answer the question, you could probably use MrBUMP to do this, using the
local PDB file option. It will require a bit of scripting to deal with all the
file names, and will take forever.
Other points:
1) you don't nee
e are interested in
> script because that dataset that we are handling is large.
> I thank you all in advance for your help.
> Best,
>
> Krishan
--
***
*
I thought so too It seems to me that there is a typo in the spacegroup
name in the code. I'll send you some fixed files offline.
Ronan is the expert on queueing systems, but I though the keyword "CLUSTER"
should be enough. It is supposed to work with SGE. There also seems to be an
undocume
Can you post details of versions. Version of CCP4. Version of Phaser (look at
top of log file).
At one point, the interface was lagging behind the program, but should be ok
now.
Martyn
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ylva
Lindqvist
Sent: 28 May 2011 13:31
As well as pdbset, you can use pdbcur. A combination of keywords genunit, symop
and symcommit.
I’d probably use genunit (applicable to whatever spacegroup you have), followed
by a second call using symop/symcommit to apply unit cell translations.
Cheers
Martyn
From: CCP4 bulletin board [mailto:
tion?
> >
> > BTW, is that simulator annealing not suitable for low resolution
> > structure? I used the simulator annealing method of CNS and
> > phenix.refine, but the geometry of the structure is always destroyed
> > seriously.
> >
> > Could you help me?
> >
> > Thank you very much!
--
*
ommand would be much quicker.
>
> Thanks.
>
>
> Andreas
>
>
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laborato
a definitions?
>
>
> Thanks justin
>
>
--
***
* *
* Dr. Martyn Winn *
*
Well, yes, that's how I would do it (but with Emacs).
But I guess the official way would be with Reflection Data Utilities -> Edit
MTZ Datasets which will edit the dataset cells. It wraps keywords of CAD.
Martyn
-Original Message-
From: CCP4 bulletin board on behalf of Ed Pozharski
Sent
Your format string works for me. It's hard to say what has gone wrong without
seeing how you ran it. Perhaps you could send me the complete log file?
If you choose column type X X-plor Rfree, then it should convert automatically
between the conventions.
HTH
Martyn
-Original Message-
Fr
Described at:
http://www.ccp4.ac.uk/dist/html/refmac5/keywords/xray-principal.html#scal
Simple scaling doesn't take into account the bulk solvent at all, whereas
Babinet is a simple fix. A more sophisticated treatment of bulk solvent is
given by the SOLVENT keyword:
http://www.ccp4.ac.uk/dist/ht
Comparing to one of my refmac jobs, it is slightly different because of
different system and options. However, I would guess that the missing labels
are:
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
But don't take my word for it - c
one have any ideas on what is going
> wrong? I see one similar message in the archives, but there were no
> responses at that time.
>
> Thanks.
>
> -ben
>
> --
> | Ben E
D Scholar
> Crystallography Laboratory
> Division of Protein Science & Engg.
> IMTECH , Chandigarh, INDIA
--
***
*
o accept both?
> Eleanor
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-m
> does part of what I intend to do.
>
> Thanks a lot,
> Francois.
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +
a-gathering protocol where exposure increased over time.
>
> Tom
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, War
Thank you for your time!
>
> Best wishes,
> Thomas
--
***
* *
* Dr. Martyn Winn *
*
and how
> can I print my total B factors.
>
>
> Thanks
> Regards
> Shiva Kumar
--
***
* *
* Dr. Martyn Winn
HOLE region define by
> the section range?
>
> Thanks!
>
> Best Regards, Hailiang
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury
ewert (Vorsitzender), Ulf
> Bialojahn, Dr. Matthias Braun,
> Peter Guenter, Prof. Dr. Dr. Werner Kramer, Dr. Klaus Menken,
> Dr. Heinz Riederer
>
> *
>
>
Actually, zero spacegroup should be tolerated by the CCP4 library now.
We were recently alerted to another problem, caused by non-zero origin in the
EM map header. But I think this is different to the problem of the original
poster.
It's probably fair to say we haven't tested enough against rea
bytes" that spell "MAP ", or a value of nsymbt that indicates
> the
> presence of additional symmetry information following the
> header, which
> is then missing.
>
> Chimera ignores most of these issues.
>
> -Christoph
B 3.' 'B 3.' C2
> RANGE 'B 3.' 'B 3.' O2
> RANGE 'B 3.' 'B 3.' N3
> RANGE 'B 3.' 'B 3.' C4
> RANGE 'B 3.' 'B 3.' O4
> RANGE 'B 3.' 'B 3.' C5
> RANGE 'B 3.' 'B 3.' C6
>
> I guess I've got the syntax of
ot for such a
> small molecule).
>
> Kind regards, Tim
>
> P.S.: The bug in pdbset persits also in pdbset from ccp4-6.1.3
>
--
*******
* *
*
n't help with Coot problems, but I will clean up
CCP4 Fortran programs at least.
m
--
***
*
s
>
> Dr Alan Roseman
> Tel: + 44 (0) 161 275 7226
> Email alan.rose...@manchester.ac.uk
--
*******
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4A
Yes, this script should work. You can also use OUTPUT CNS.
But the GUI is not up-to-date with the program. This is fixed now. You
can pick up fixes via the Problems Page
http://www.ccp4.ac.uk/problems.php#6.0.2-export-hl
or it will be in the next release.
Tip for newbies: you can always get arou
[posted on behalf of Lydia Tabernero]
UNIVERSITY OF MANCHESTER
FACULTY OF LIFE SCIENCES
POST DOCTORAL RESEARCH ASSOCIATE
This post offers an excellent opportunity to join a dynamic research
team in the Structural Biology group o
On Fri, 2007-02-23 at 11:08 +, Roberto Steiner wrote:
> There is something wrong with COM (actually I do not understand why
> it is COM_COM rather than COM?
> Alexei? Garib?)
Basically because Windows platforms get confused with things called COM.
PRN_PRN.cif is another one.
Martyn
I wouldn't call it numerical error, as such. Refmac doesn't
restrain/constrain the T, L or S values at all. In particular, the L
value can refine stably and accurately to a negative value.
Refmac is refining a set of ADPs constrained to fit a certain functional
form with parameters T, L and S. Th
A glance through the CVS history of mtz2various and f2mtz shows that
there has been a lot of work keeping these up-to-date for various
formats, work that is largely unrewarded and unacknowledged. But they
are indeed still deficient in places.
The required code writing is relatively trivial. The ha
ption to write F's is
> >> still needed, in which case there needs to be a way of specifying this.
> >>
> >> - The user should be very strongly discouraged from re-squaring the
> >> F's from Truncate (possibly even by removing the FSQUARED optio
Hi Ian,
Thanks for your helpful analysis. There are now updated versions of the
source code and the documentation at:
ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches/mtz2various-r1_130.f
ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches/mtz2various-r1_39.html
or via the Problems Pages. In particular:
1. The foo.
PS Meant to say, I am aware the GUI doesn't give you the option to
specify I for SHELX. Will fix in due course (meanwhile Run&View Com)
m
On Tue, 2007-03-06 at 13:43 +0000, Martyn Winn wrote:
> Hi Ian,
>
> Thanks for your helpful analysis. There are now updated versions of
CCP4 is a collaboration between many and varied authors, so the exact
answer depends on which bit of the ccp4 interface you are talking about!
Generally, most CCP4 programs will work with "standard" PDB files. The
spacegroup on the CRYST1 line is only needed if a program can't get the
symmetry inf
[Posted on behalf of Lydia Tabernero. Full text of this posting
available here: http://www.ccp4.ac.uk/martyn/MSc-Leaflet.doc ]
1 year MSc in Structural Biology and Biophysics at Manchester, UK,
starting in September 2007
Aims & Objectives: Structural and biophysical analyses are essential in
unde
These are under "TLSANL" i.e. for analysing TLS parameters (1st is the
program reference, second is the original TLS formulation).
For TLS _refinement_ look under "refmac".
If you used TLSMD, then there are separate references for that.
Regards
Martyn
On Wed, 2007-05-09 at 09:25 -0400, Nalam, Ma
The level of detail in the GUI is a matter of constant debate. The
underlying programs are far far richer, so the question is how much to
expose in the GUI. We try to get a balance between ease-of-use and
coverage, but it won't always work. BTW I don't think we ever claimed
that ccp4i (or anything
al
> expert GUI-mode. Users should be able to choose one or the other in
> their defaults, or switch from one to the other on-the-fly.
>
> I don't have a particular problem in editing the scripts as it is done
> now, but I have found that students tend to get a bit nervous about
&g
. unless you
> > mean that it can happen that options that become outdated disappear from
> > the program, so there would be a risk of having their "ghosts" in the
> > GUI. But normally programs complain when an option is not available,
> > don't they?
>
Thanks Pierre. Its good to have more than one idea.
I'd had a similar private idea - basically to have a pull-down menu of
all keywords (there's a slight issue that ccp4i tasks tend to include
several programs).
My feeling is that segregating the expert options into folder(s) under
global control
The CCP4 program rwcontents includes the data from
Carugo & Bordo, Acta Cryst D, 55, 479 (1999)
Headline figures are 1.0 waters per protein residue at 2.0A, and 1.6-1.7
waters per protein residue at 1.0A. They use mainly room temperature,
but also some cryo structures.
And, as Clemens said, you s
This parameter is MAXTLSGRP in $CCP4/src/refmac5_/tls.fh
You can increase it here BUT you have to then re-compile Refmac.
It doesn't have phenix.refine's dynamic allocation ;-(
Note that it is already increased to 200 in Refmac 5.3 available from
York or from http://www.ccp4.ac.uk/prerelease/
H
> tlsanl) to work?
>
> Cheers,
>
> Craig.
>
--
***
* *
* Dr. Martyn Winn *
*
his breaks of
> ploting or in case of mlphare of the whole process.
>
> Does anybody know how to handle this? Is it related to the OS or to
> CCP4?
>
>
> Thanks for helping another time justin
>
--
******
? ? ?
> ? ? ? ? ? ?
> ?
> -47 1 20.00 0.00
> 0.00 ? ? ?
> ? ? ? ? ? ?
> ?
> -47 1 3 17.00 0.00
> 0.00 ? ? ?
>
> >>>
> >>> ... then pointless reports :
> >>>
> >>> Selecting space group P 41 21 2 as solutions are enantiomorphic
> >>> Best Solution space group P 41 21 2
> >>>
> >>> ... is that b/c pointless can only report one, and SG92 came up
> >>> first?
> >>>
> >>> -bryan
> >>
> >>
> >
--
|In UK add 0 to start of number
> Fife Scotland, U.K., KY16 9ST|http://www.st-and.ac.uk/~strucbio
>
--
***
*
tain it?
>
> Regards,
> Patrick Hollerein
--
***
* *
* Dr. Martyn Winn *
*
; >
> >
> > This message was sent using IMP, the Internet Messaging Program.
> >
--
*****
(as a part of the main
CCP4 in the choice).
Enjoy!
Martyn
--
***
* *
* Dr. Martyn
bring own data.
*'
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warr
ain lectures ?
>
> Thank you very much in advance for any useful links !
>
> Juergen
>
--
***
* *
*
lee (Leuven)
> > Tel: +32(0)16327477
> > --
> >
> >
> >
> >
> >
> > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
> >
--
***
* *
* Dr. Martyn Winn
>> > N 1.10 ±0.17
> >> >
> >> > K 1.49E5 ±1.5E5
> >> >
> >> > DH -893.5 ±213
> >> >
> >> > DS 20.7
> >> >
> >> > Was the enthalpy was offset by the ionization of Tris buffer?
> >> >
> >> > Can I use Hepes buffer around pH8 to
==
> David J. Schuller
> modern man in a post-modern world
> MacCHESS, Cornell University
> [EMAIL PROTECTED]
--
*****
.
> Lawrence Berkeley National Lab, Berkeley CA, USA (http://www.lbl.gov/)
> CCI: Computational Crystallography Initiative (http://cci.lbl.gov/)
> PHENIX (http://phenix-online.org/)
>
&g
susceptible to data corruption, interception, unauthorized
> amendment, and tampering, Astex Therapeutics Ltd only send and receive
> e-mails on the basis that the Company is not liable for any such alteration
> or
;> Institut fuer anorganische Chemie
> >> Tammannstr. 4
> >> D-37077 Goettingen
> >>
> >> GPG Key ID = A46BEE1A
> >>
> >>
> >>
> >> On Tue, 10 Jun 2008, john kryst wrote:
> >>
> >>
binary.. pls help me out
>
> John
--
***
* *
* Dr. Martyn Winn *
*
nt bioxhit ,oulu workshop)
> > where can i get them, is there any scientist ready to provide.
> >
> > --
> > S.Jayashankar
> > Research Student
> > Institute for Biophysical Chemistry
> > Hannover Medical School
> > Germany
--
***
on a stick?
>
> Looking forward to your responses.
>
> Regards,
>
> Dave
--
***
* *
* Dr. Martyn Winn *
* *
* STF
the addition of
> d-orbitals to the mix). So, Na+, Mg2+ are generally OK, Ca2+, Fe, Mn,
> etc. are much more tricky, especially in a quick and dirty simulation.
>
> On Thu, 2008-07-03 at 12:20 +0100, Martyn Winn wrote:
> > Gromacs www.gromacs.org
> >
> > It is GPL.
7;Parameter MAXSAVE exceeded''
>
> --
> S.Jayashankar
> Research Student
> Institute for Biophysical Chemistry
> Hannover Medical School
> Germany
--
***
*
ccp4spg_register_by_symops
>
> Does anybody know how to fix it?
>
> Petr
--
***
*
Cheers ;-)
Martyn
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrin
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury
_
> 使用 MSN 有问题怎么办？客服机器人来帮忙！
> http://help.msn.cn/
>
--
***
* *
* Dr. Martyn Winn *
*
> The Famous, the Infamous, the Lame - in your browser. Get the TMZ
> Toolbar Now!
--
***
* *
* Dr. Martyn Winn *
*
(lots of)
Feedback to the usual locale ([EMAIL PROTECTED])
Thanks
Charles and the rest of us here at DL.
--
***
* *
* Dr. Ma
on 1, 1070 Brussels (Belgium)
> tél: +32 (0)2 5273634
> fax: +32 (0)2 5267273
>
--
***
*
324.4280.189
> ADP C3*CCH1 0.000 -2.0904.668 -1.916
> ... etc
>
> Should these dictionaries be changed?
>
> Phil
--
****
ular Biology (BCMB)
> University of Tennessee -- Knoxville
> 216-368-3337 [EMAIL PROTECTED] [EMAIL PROTECTED]
>
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***
*
email. E-mail is susceptible to data corruption, interception, unauthorized
> amendment, and tampering, Astex Therapeutics Ltd only send and receive
> e-mails on the basis that the Company is not liable for any such alteration
> or any consequences thereof.
> Astex Therapeutics Ltd., Re
>
> if you take a look at the ftp servers, you will already find the 6.1
> packages, although there is no release announcement yet.
>
> ftp://ftp.ccp4.ac.uk/ccp4/6.1/
>
>
> Thanks,
> justin
>
>
>
--
***
invoked from within
> ".w_sftools_PROJECT.main.canvas.contents.param_1.top.but invoke"
> (command bound to event)
>
> Any ideas?
>
> Engin
--
***
* *
*
; University of Colorado
> jonathan.caruth...@colorado.edu
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laborator
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