site?
e
On 4 September 2013 22:57, Garib N Murshudov ga...@mrc-lmb.cam.ac.uk wrote:
Hi
refine bref bonly
should be what you are looking for. You may need to use the latest available
version (5.8) from our LMB site:
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
With best regards
Hi Bill,
I will add it tomorrow. However with new ccp4 release source code update should
be straightforward (I hope).
Regards
Garib
On 5 Sep 2013, at 15:15, William G. Scott wrote:
On Sep 4, 2013, at 2:57 PM, Garib N Murshudov ga...@mrc-lmb.cam.ac.uk wrote:
You may need to use
CGMAT -
bref anisoonly
ncyc 5
As far as Bill Scotts question does coot not pick up refmac5 and libcheck
from $CCP4_BIN ?
Thanks
Hari
On Thu, Sep 5, 2013 at 10:15 AM, William G. Scott wgsc...@ucsc.edu wrote:
On Sep 4, 2013, at 2:57 PM, Garib N Murshudov ga...@mrc-lmb.cam.ac.uk
refine-
bref aniso bonly
This also works ( I was just guessing before I saw your previoud email) but
It probably is equivalent to the one above.
refine-
bref anisoonly
Thanks for your help
Hari
On Thu, Sep 5, 2013 at 11:24 AM, Garib N Murshudov ga...@mrc
without changing the model
coordinates .
Is this accomplished using a zero cycle refinement with b-refinement set.
I have never had to do this till now and didnt know how to set it up.
Thanks
Hari
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
something?
Any help muchly appreciated. (I am using the most upto date version of the
CCP4 package on a PC)
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web
a problem with the structure of the N-terminal
capsid domain of HIV-2 PDB 2wlv.
Load it up to in coot and navigate to residue B118.
/Michel.
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge
CB2 0QH UK
Email: ga
is not needed at compile time. Files like
environ.def and
default.def are read at this time. Perhaps there has been a corruption of one
of these
files or you are pointing to an earlier version of $CINCL. Does the error
occur with
refmac alone or with every CCP4 prog?
Adam
Dr Garib N
://enigmail.mozdev.org/
iD8DBQFRAkzvUxlJ7aRr7hoRAlVfAKClRD4/JLNDcOab1HjBroQYXND3bQCfegA9
UiHvuKXg2/b3LqlbPWQpKmY=
=Awum
-END PGP SIGNATURE-
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc
/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iD8DBQFRARtHUxlJ7aRr7hoRAnvXAKCqUV5IHvKJShQHrN8/cCGmC4DDrACgw9gL
6MGqgIDK4DJ2vcHtuzdWPBc=
=Pl4P
-END PGP SIGNATURE-
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2
will automatically
switch to the proper flags, so this problem should go away.
-Nat
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
similar.
Thank you again for your help.
Andrea
Quoting Garib N Murshudov ga...@mrc-lmb.cam.ac.uk:
Dear Andrea
There are two ways as they were mentioned by Tim and Ian:
1) Using external restraints mechanism. You define something like (it is an
example):
external plane first
!
Andrea
Andrea Pica, Ph.D. student
University of Naples Federico II
Department of Chemical Sciences - Room 1N-04
Complesso Universitario Monte S. Angelo
Via Cintia
I-80126 Naples - Italy
Phone 39-081 674269
Fax 39-081 674090
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular
for your help.
Best wishes,
Q. Cai
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
.
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Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
pdb file and i keep getting this error with refmac
ERROR: number of chains 1500
i suspect something needs to be done to my pdb
any suggestions ?
thanks
jpd
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
.
I am sure there are many ways do it. My friend would appreciate if you could
simplify and explain this so that he could learn it without difficulties.
Also I could learn
I appreciate your time and help
Thanks
Rajesh
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
--
Deepthi
--
Deepthi
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
is shooting up to 0.41. It is not accepting any changes to
the Phenix generated model. I have no idea what is going on. Can anyone help
me?
Thank You in advance
Deepthi
--
Deepthi
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
for Structural Biology
Division of Molecular Biosciences
Level 5 Sir Ernst Chain Building
South Kensington Campus
Imperial College London
London SW7 2AZ
Tel: +44 (0) 207 594 5464
Fax: +44 (0) 207 594 3057
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
becomes 52% and 42% respectively
in Refmac with all the solutions.
I will highly appreciate all the suggestions for this kind of problem.
Thanks and regards
--
Sonali
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga
-to-parameters ration.
-Nat
B_versus_d_min.png
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
continue
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
Is that what you are looking for?libcheck cn generate it (JLigand should be able). grade should also generate from smiles.Garib
1.cif
Description: Binary data
1.pdb
Description: Binary data
On 9 May 2012, at 17:08, Shya Biswas wrote:Hi all,I am having trouble generating a pdb and cif file from
Department of Biochemistry Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab: +1-410-614-4894
Fax: +1-410-955-2926
http://web.mac.com/bosch_lab/
Dr Garib N Murshudov
Group Leader
curious what
the bump around 2.25A is.
-Nat
wilson_highres.png
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
anyway...
JPK
On Wed, May 9, 2012 at 2:08 PM, Nat Echols nathaniel.ech...@gmail.com wrote:
On Wed, May 9, 2012 at 11:58 AM, Garib N Murshudov
ga...@mrc-lmb.cam.ac.uk wrote:
As far as I know there are several bumps: around 3.5-4 (there are some at
low resolution related with molecular
Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
about changing the bulk solvent treatment to better account
for solvent contribution inside the protein cavities?
Best wishes, and thanks in advance for all your help,
- Allister Crow
bulk_solvent_inside_cavities.png
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular
or not.
Keitaro
2012/4/16 Garib N Murshudov ga...@mrc-lmb.cam.ac.uk:
Dear Allister
Could you please update refmac version. In the version you it seems that
bulk solvent mask calculation has some problems. New version (at the moment)
can be downloaded from this site:
http
it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL).
But I'm not sure that FC_ALL = FC + FMASK is correct or not.
Keitaro
2012/4/16 Garib N Murshudov ga...@mrc-lmb.cam.ac.uk:
Dear Allister
Could you please update refmac version. In the version you it seems that
bulk solvent mask calculation
option?
I have not tried but if you can use vector difference map then it should be:
FMASK = FC_ALL_LS - FC
What is FC_ALL in the new version?
Thanks,
Keitaro
2012/4/16 Garib N Murshudov ga...@mrc-lmb.cam.ac.uk:
A follow up:
In the new version there is FC_ALL_LS, PHIC_ALL_LS
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
://web.mac.com/bosch_lab/
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
large. Would you think it's safer to
integrate the data in P1 as symmetry mates will not be merged and then solve
in P1 and convert into P21 cell for further refinement afterwards ?
Jürgen
On Mar 27, 2012, at 4:53 PM, Garib N Murshudov wrote:
I would say that you should use ncs
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
Garib N Murshudov
be doing
these things? If yes, then what is the best way of doing it?
Your suggestions and corrections to my interpretation of our data would be
appreciated.
Regards
Shiva
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
them.
Could you please suggest me some options.
Thanks
Rajesh
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
.
Thanking you
With Regards
Kavya
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Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
/email.htm
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
et Chimie des Protéines
Drug-resistance modulation and mechanism Laboratory
7 passage du Vercors
69007 LYON
FRANCE
+33 4 37 65 29 01
http://www.ibcp.fr
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc
the remaining two copies even there are
strong fo-fc density?
Any suggestions...
Thanks a lot!
Zhihong
weird thing.jpg
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc
-END PGP SIGNATURE-
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
defined?
Can the hydrogen behavior in REFMAC be more explicitly controlled.
Thanks,
--Paul
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
, the input file had 0 ... 19. During
the first run, Rfree dropped to 28%. But on a subsequent run, Rfree was
stuck 30% when I used the initial job's output MTZ.
Many thanks in advance for your helpful comments.
Wolfram Tempel
Garib N Murshudov
Structural Studies Division
MRC Laboratory
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa
Ph / Waea +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
for example?) solves this problem. Presumably such
software is used to show several overlaying ligand structures (all
called LIG?). And computational chemists like to see chemistry, and
not just coloured sticks, right?
Thanks,
Paul.
Garib N Murshudov
Structural Studies Division
MRC Laboratory
/newsoffice/2012/faster-fourier-transforms-0118.html
--
Jim Fairman, Ph D.
Crystal Core Leader I/Project Leader I
Emerald BioStructures
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com
Garib N Murshudov
Structural Studies Division
MRC Laboratory
structure and crystal packing
between P212121 and P1 after MR, and the electron densities followed trace of
peptide chain well.
Can anybody suggest me about this problem?
Thank you.
Ki Joon Cho
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
Mailing address :
Instituto de Tecnologia Quimica e Biologica
Apartado 127
2781-901 OEIRAS
Portugal
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
1.2600.020
I appriciate your help beforehand.
Regards
Sam
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
does not resemble 3'-GMP at all.
Yours
Wolfgang
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
; formerly 5.6.0117),
libcheck is 5.2 (formerly 5.1.14),
dictionary is 5.28
I also tried each of the four refmac5-libcheck combinations, but without
success.
yours
Wolfgang
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
--
Structural Biology Group / Department of Molecular Biology
University of Salzburg
Billrothstraße 11
5020 Salzburg
Austria
Phone: +43 662 8044 7278
http://www.uni-salzburg.at/xray
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH
instead
of simple.
Yep, understood.
Thx, BR
Regards and Happy New Year
Garib
From: Garib Murshudov [mailto:garib.murshu...@gmail.com] On Behalf Of Garib N
Murshudov
Sent: Thursday, December 29, 2011 4:47 PM
To: b...@hofkristallamt.org
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb
2 Ks and Bs.
So I conclude that ‘overall’ and ‘partial’ lines do not list Babinet ks and
Bs (the B is also too small for that)
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http
Browning
--
Dr. Christopher Browning
Post-Doctor to Prof. Petr Leiman
EPFL
BSP-416
1015 Lausanne
Switzerland
Tel: 0041 (0) 02 16 93 04 40
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web
is coordinated to the
spot of the closest contact), how can I disable it?
Cheers,
Ed.
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs
Garib N Murshudov
Structural Studies Division
MRC
with this side chain?
Thanks for any assistance
Careina
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
is the only way?
Thank you very much for any comments!!
With best regards,
Ivan Shabalin, Ph.D.
Research Associate, University of Virginia
4-224 Jordan Hall, 1340 Jefferson Park Ave.
Charlottesville, VA 22908
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
the
old ccp4 and refmac to publish. Rf 17 R 15.
thanks
--
Kenneth A. Satyshur, M.S.,Ph.D.
Associate Scientist
University of Wisconsin
Madison, Wisconsin 53706
608-215-5207
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iD8DBQFOqluhUxlJ7aRr7hoRAjadAJ9Df2hbWjixDCdS3Z4DB7mm4ubRIACeOw6X
6JkjyzRUdxqjH/9b/oftBjE=
=xRXE
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Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
of the audience is
telling
With respect to existing density modification programs, I wonder if such
technology (whatever it is) can ever clear up my messy density maps.
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
Garib N Murshudov
E-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http
not done any tests
but on paper it looks like a sensible procedure.
regards
Garib
On 11 Oct 2011, at 20:58, Ethan Merritt wrote:
On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
In the limit yes. however limit is when we do not have solution, i.e. when
model errors are very
58.7097
1.3041
Eleanor
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
Is there any documentation for this?
E
On 10/04/2011 03:56 PM, Garib N Murshudov wrote:
If you will put element names in correct positions then refmac may have a
chance to find it. Here is corrected positions:
ATOM 1893 O HOH A 258 -8.934 52.268 49.467 0.00 66.53
generated mtz with PHIC and FOM information?
Thank you
--
Yuri Pompeu
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
DETWIN with the estimated 0.46 alpha, my completeness for the
detwinned data is now down to 54%!!!
Is this normal behavior? (I am guessing yes since the lower symmetry
untwinned dat is P1 21 1)
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
and profound brain things inside my head,
I have decided to thank you for bringing peace to our home.
Julian, King of Lemurs
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
Garib N Murshudov
letters for RNA?
F
On Sep 12, 2011, at 1:05 PM, Garib N Murshudov wrote:
Refmac will read right or left justified residue names, however pdb may use
only one of them.
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
mapmask itself dies in the middle of running and without error message
to its log file.
thanks
ingo
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
by models
with 25 % sequence identity and 30 % sequence similarity.
Thank you so much for reading this mail during your busy hours and
all suggestions, comments would be gratefully welcome appreciated.
thank you ccp4 mailing list.
John
Garib N Murshudov
Structural Studies Division
MRC
/
iD8DBQFOVgiBUxlJ7aRr7hoRAq+dAKDj2B6iUMD7C4uu8UMznTlKoclYzACdF8nP
Q6DmIFGPcfoP6xbJRwooWWI=
=7r5T
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Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc
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Version: GnuPG v1.4.11 (GNU/Linux)
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iD8DBQFOVReTUxlJ7aRr7hoRAqyzAKCZpMJPVSQJTDEoWGxZEymwvqfFcACeMNLL
rvIDPlXiL5HQmoNm7yrTt6k=
=UnKT
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Garib N Murshudov
Structural Studies Division
MRC
...@cornell.edu
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
Dear AfshanMake sure that group name for CME is peptide (or L-peptide). In the new version CME is peptide. I am not sure it was the case in older versions. I attach CME as a peptide. You can add this into your dictionary.Then CME can become part of a peptde. It would also be good to remove all the
External distance restraints have type
type 0 - replace what is generated by refmac
type 1 - use if there is no restraint for this type. Only one restraint per
atom pair
type 2 - there may be many restraints per atom pair. Refmac will choose the
restraint that is the closest to current
Dear Petr
Newer version of refmac is 5.6 and it should be available from ccp4 soon.
Meanwhile you can try this version from this website
http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.6_linux.tar.gz
There are versions for mac etc also.
regards and I hope you will sort
If you are using TLS refinement the please check TLS definitions.It may be that
atoms for which you have positive density are not in TLS definitions.
Try to use without TLS.
regards
Garib
On 26 May 2011, at 11:11, Petr Kolenko wrote:
Dear colleagues,
I have two problems in two structure
It should be remembered that refining in real space is equivalent to refinement
in the reciprocal space (through Parseval's theorem). If you want to do
consistent refinement then you need to use exactly same reflections for free
and working set. If you do not use the same set of reflections
It does not matter. By fitting manually you are doing manual minimisation. The
same treatment is applied. You are trying to optimise fit of the model into the
electron density.
I did these tests few years back and results were as expected. Independent on
minimisation tools (manual, automatic,
Dear Keitaro
As far as I know different program behave differently. REFMAC by default
replaces structure factors of the excluded reflections with their expected
values (as a first approximation) that is equal to DFc, where D reflects errors
in coordinates. It seems to be a balance between
Dear Geoff
Perhaps you could try jligand available from:
http://www.ysbl.york.ac.uk/mxstat/JLigand/index.html
There are few tutorials how to deal with ligands and links.
I hope it helps
Cheers
Garib
On 20 May 2011, at 21:59, Geoffrey Feld wrote:
Greetings fellow Crystallographers,
I'm
Dear Mary
It should not be unless you ask specifically using one of the following keywords
mapc sharpen # automatically define sharpening parameters
mapc sharpen bvalue # use this bvalue for sharpening with automatic
regularisation parameter
mapc sharpen alpha value # sharpen with
It seems that there is a mismatch between dictionary and libcheck versions.
Could you please check
1) library
vi $CLIBD_MON/a/ADN.cif
It should have primes like:
ADN O2' OOH1 0.000 0.0000.0000.000
ADN HO2' HH 0.000 0.731 -0.600
I would not sharpen structure factors before refinement. It may cause problems
with B value refinement (a lot of B values may stuck around 2 or minimum B).
One must remember that not all atoms in crystal have same Bvalue. There is a
distribution of Bvalues.
However maps can be sharpened after
trying to re-refine and then
re-submit the more correct structure to the PDB.
Yury
On Thu, 10 Feb 2011, Garib N Murshudov wrote:
Maximum theoretical drop R/Rfree for perfect twin from 30% is around 25%
(i.e. it could go down to 5%). However it could only happen only if twinning
and then
re-submit the more correct structure to the PDB.
Yury
On Thu, 10 Feb 2011, Garib N Murshudov wrote:
Maximum theoretical drop R/Rfree for perfect twin from 30% is around 25%
(i.e. it could go down to 5%). However it could only happen only if twinning
is perfect
molrep can deal with some of the PST cases.
Garib
On 9 Feb 2011, at 22:27, Phil Jeffrey wrote:
Is there a program that does ? I was under the impression that they were all
equally good/bad at this, because any solution that agrees with the PTS has
quite a high score and any solution that
It indeed seems to be case. Thank you for pointing this out. I have change in
the version I have and it will be available soon.
reagrds
Garib
On 20 Jan 2011, at 14:26, Thomas Womack wrote:
The restraint dictionary for hydrogenated tryptophan,
lib/data/monomers/t/TRP.cif, lists a 15-atom
Dear Marcus
The most likely reason is that geometry is a bit loose. You need to tighten it
a bit.
You can do by decreasing weight using weight matrix option on the interface.
You need also check the electron density to make sure that ILE is in electron
density.
Please let me know if you
Hi
they are in the standard dictionary. To make sure that you have full range of
ligand you may take the dictionary from
www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac_dictionary_v5.23.tar.gz
and corresponding refmac
Dear Yu
I cannot say about other programs. refmac uses equation in slides No 13-14 of
the presentation:
http://www.ysbl.york.ac.uk/refmac/Presentations/ Refmac_Erice_workshop.ppt
If your crystal is a perfect twin and you have processed data in true space
group then refmac will give map for a
At the moment there is no way of telling refmac to ignore clashes between
symmetry related atoms.
Is there any reason you would want to do that? Perhaps there are other ways of
solving the problem you would like to solve.
I can add a keyword to force to ignore these clashes if there is
In refmac you can remove vdw interactions between chains using the following
command
It is an example:
vdwr exclude between chains A B
or between resdues:
vdwr exclude between residues first residue 123 chain A second residue 155
chain B
Regards
Garib
On 8 Dec 2010, at 16:09, Keitaro
. Yamashita
2010/12/9 Garib N Murshudov ga...@ysbl.york.ac.uk:
In refmac you can remove vdw interactions between chains using the following
command
It is an example:
vdwr exclude between chains A B
or between resdues:
vdwr exclude between residues first residue 123 chain A second residue 155
If you will replace link line with the following
LINKRC1 NAG A1003 ND2 ASN A 611NAG-ASN
Then it should be read by refmac and by coot. And restraints should be applied
properly
regards
Garib
On 2 Dec 2010, at 06:49, Dr. STEPHEN SIN-YIN, CHUI wrote:
Dear All
New version of jligand - version 1.0.0 is now available to download and use. It
can be downloaded from
http://www.ysbl.york.ac.uk/mxstat/
There are also tutorials how to jligand to create ligand and link descriptions.
jligand is a program to create new ligand descriptions. It also
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