isoonly
>
> Thanks for your help
> Hari
>
>
>
>
>
>
>
> On Thu, Sep 5, 2013 at 11:24 AM, Garib N Murshudov
> wrote:
> You do not need anisoonly. You need bref only. If input pdb has aniso card
> then refmac will assume that mixed refinement should b
-
> resi MLKF -
> meth 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 wrote:
> On Se
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 wrote:
>
>> You may need to use the l
at web site?
> e
>
> On 4 September 2013 22:57, Garib N Murshudov 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
quot;B"s in refmac 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
>
>
>
>
>
tch the external
> restraints or cif file. Am I missing 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
Cambri
t; Sent: April-12-13 1:14 PM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] Puzzling Structure
>>
>> Has anyone else noticed a problem with the structure of the N-terminal
>> capsid domain of HIV-2 PDB 2wlv.
>>
>> Load it up to in coot and nav
error
> occur with
> refmac alone or with every CCP4 prog?
>
>
> Adam
>
>
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
--
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>
> iD8
version of Refmac 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
t;>>>>
>>>>>
>>>>> My question is, why B-factor gone up now and R/Rfree reduced.
>>>>> In which refined model should I believe in. If last refined
>>>>> model is true then how should I reduce the B-factor?
>>>>>
>>>>> Thank you Rajesh
>>>>>
>>
>>>
>>
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/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 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
X1+X2 chain B residue 50
> or something similar.
>
> Thank you again for your help.
>
> Andrea
>
>
>
> Quoting Garib N Murshudov :
>
>> Dear Andrea
>>
>> There are two ways as they were mentioned by Tim and Ian:
>> 1) Using external restraints
> Thank you very much!
>
> 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
s are estimated, they seemed to
be better than nothing.
regards
Garib
>
> Thanks very much 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
30, 2012, 3:43 PM
>
> hi,
> i have a large 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 Molecul
t;>>
>>>
>>
>> - --
>> Dr Tim Gruene
>> Institut fuer anorganische Chemie
>> Tammannstr. 4
>> D-37077 Goettingen
>>
>> GPG Key ID = A46BEE1A
>> -BEGIN PGP SIGNATURE-
>> Version: GnuPG v1.4.12 (GNU/Linux)
>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>>
>> iD8DBQFQj5K5UxlJ7aRr7hoRAum6AKDzlXQSoX827+OrPJOiWy1zF24pVgCgymMq
>> Hgv5aAxCqVjSnONml1GSfx0=
>> =KVPK
>> -END PGP SIGNATURE-
>>
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
>>
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
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
ith covalent bond.
> 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 Mursh
ated some residues which don't align with the model protein to
>> Alanines. When i change the residues back to their respective side chains
>> Refmac5 won't refine it well. The maps looks clear( you can guess its 1.4A0
>> data) but R-free 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
>
>
>
>
> --
> 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
hen i change the residues back to their respective side chains
> Refmac5 won't refine it well. The maps looks clear( you can guess its 1.4A0
> data) but R-free is shooting up to 0.41. It is not accepting any changes to
> the Phenix generated model. I have no idea what is going o
90.0 51.590.0 360.0 90.0
>1. 0. 0.
> 4 2 270.0 90.0 270.0 51.5 135.0 90.0 180.0
>0. 0.7070 -0.7072
> 4 3 90.0 90.0 270.0 51.590.0 180.0 90.0
>
st even 10 or more but no good electron
> density map yet. Free R and figure of merit 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
>
> --
&
ge anything in refinement,
> aside from making it easier because you have a better
> observations-to-parameters ration.
>
> -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
1 CC is missing in the structure
> ATTENTION: atom:C3 GUA 1 CC is missing in the structure
> ATTENTION: atom:C1 GUA 1 CC is missing in the structure
> ATTENTION: atom:O1 GUA 1 CC is missing in the structure
> ATTENTION: atom:O2 GUA 1 CC is missing in the structure
>
> ===> Error: Fatal error. Cannot 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
y implicit in molecular replacement
> anyway...
>
> JPK
>
> On Wed, May 9, 2012 at 2:08 PM, Nat Echols wrote:
> On Wed, May 9, 2012 at 11:58 AM, Garib N Murshudov
> wrote:
> > As far as I know there are several bumps: around 3.5-4 (there are some at
> > low resolution re
s (of different proteins). I'm curious what
> the bump around 2.25A is.
>
> -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
lic Health
> 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/
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 t
> Tel: +1 203 432 9576
> Fax: +1 203 432 6144
> www.baxterlab.org
> =
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
what might be going on.
> I used SAD function.
> What does it mean?
>
>
> Cheers,
>
> Keitaro
>
> 2012/4/17 Garib N Murshudov :
>> Dear Ketaro
>>
>> At the moment mskout option is a signal that the program should stop.
>> Obviously I can add an
y way to do refinement with mskout 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
ied to generate 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 :
>> Dear Allister
>>
>> Could you please update refmac version. In the ver
to generate 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 :
>> Dear Allister
>>
>> Could you please update refmac version. In the version you it se
g substantial changed in the bulk solvent treatment between
> Refmac versions 5.5 and 5.6?
>
> 2) How can I go 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 h
inement?
> Suggestions greatly appreciated.
> Thanks,
> Chris
>
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
ng reflections will be too 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
cular 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/
>
>
>
>
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
David J. Schuller
> modern man in a post-modern world
> MacCHESS, Cornell University
> schul...@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
;L=ccp4bb&D=0&1=ccp4bb&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=204490)
> or refining against medium intensity reflections. Should I also be doing
> these things? If yes, then what is the best way of doing it?
>
> Your suggestions and corrections to my inte
ues ( phosphoserine and phosphothreonine).
> During refinement these both gets disconnected with adjacent residues and
> its hard to connect 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
n i use the new interface to
> run old refmac binary? Kindly provide
> some suggestion.
>
> Thanking you
> With Regards
> Kavya
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
Garib N Murshu
ojd...@york.ac.uk
> EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/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
u for your input.
> vincent
>
>
> --
> Vincent Chaptal, PhD
> Institut de Biologie 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
>
Gar
els found by Phaser.
>
> Why is that Phaser could not find the remaining two copies even there are
> strong fo-fc density?
> Any suggestions...
>
>
> Thanks a lot!
>
> Zhihong
>
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
> >
> > see "On contribution of hydrogen atoms to X-ray scattering"
> > here:
> > http://www.phenix-online.org/newsletter/
> >
> > Pavel
> >
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.11 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>
> iD8DBQFPVSXkUxlJ7aRr7hoRAm1TAJ9Hyfhkl3yhD5QSKw9I4RSK58m0fACgmlxk
> YGILzeMam/3gQVmCeh0vQ8k=
> =3m2J
> -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
scattering contributions calculated regardless of they are explicitly defined?
>
> Can the hydrogen behavior in REFMAC be more explicitly controlled.
>
> Thanks,
>
> --Paul
>
>
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hi
underestimated symmetry? And what do I
> need to know about my free-R? Did refmac assign a new flag? Whereas the
> output file's flags are all 1s and 0s, the input file had 0 ... 19. During
> the first run, Rfree dropped to <28%. But on a subsequent run, Rfree was
> stuck >30
ry
> National School of Pharmacy
> University of Otago
> PO Box 56 Dunedin 9054
> New Zealand
> Skype: jtyndall
> http://www.researcherid.com/rid/C-2803-2008
> Pukeka Matua
> Te Kura Taiwhanga Putaiao
> Te Whare Wananga o Otago
> Pouaka Poutapeta 56 Otepoti 9054
> Aotearoa
>
>
traints inside a Coot
>> molecule - that might be a cleaner solution. I will ponder on that.
>> It does mean that you will have to read restraints after reading
>> coordinates though.
>>
>> And yes, I do occasionally wonder how computational chemistry software
>> (Maestro, Vida 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 of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
gt;
> http://web.mit.edu/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
&g
There were almost no differences on monomer 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 Murshud
_chem_link_bond.value_dist
> _chem_link_bond.value_dist_esd
> LYS-MER 1 NZ 2 C18 double 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
t/research/biological-chemistry/industry-and-medicine-applied-crystallography
> http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
>
> Mailing address :
> Instituto de Tecnologia Quimica e Biologica
> Apartado 127
> 2781-901 OEIRAS
> Portugal
ovided; 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 Biol
m polyhedron which 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
current version
> of OpenJDK and Sun Java JRE 6u30; even compiling the JLigand source on my
> platform with Sun Java SE 6u30 did not help.
>
> Kind regards,
> Wolfgang Skala
> --
> Structural Biology Group / Department of Molecular Biology
> University of Salzburg
&g
> Yes, that can be done by unclicking the box "Calculate the contribution from
> the solvent region". Handy if one needs to check certain things…
>
> Ø To turn Babient's bulk solvent you need to use Babinet's scaling instead
> of simple.
>
> Yep, und
--
>
> PS: The doc leaves me a little confused because SCAL type SIMP would imply
>
> KB = K0*exp(-B0*s^2) (Simple Wilson scaling)
>
> i.e. K1 = 0
>
> while BULK (Babinet) which I did not specify
>
> KB = K0*exp(-B0*s^2) * (1-
FMAC map is fine.
>>
>> How can this be and what causes this?
>>
>> Link for the pictures:
>> Both maps are at identical Sigma levels in both pictures.
>> PHENIX: http://dl.dropbox.com/u/51868657/PHENIX_refined.png
>> REFMAC: http://dl.dropbox.com/u/5186865
ein stuff 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 Mu
> something funky is happening 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
atom type in the library, so that the scattering
> factor coefficients will be taken into account by Refmac? Or changing
> PDB-file manually is the only way?
>
> Thank you very much for any comments!!
>
> With best regards,
> Ivan Shabalin, Ph.D.
> Research Associate, Un
B mod.= 2.446 id.= 1.530 dev= -0.916
>>> sig.= 0.020
>>> A 6 LEU CB A - A 6 LEU HB2 A mod.= 0.969 id.= 1.521 dev= 0.552
>>> sig.= 0.020
>>> A
>>>
>>> Rfree goes form 17 to 28 and R from 15 to 25.
>>> Coot map looks like
>> A 6 LEU N B - A 6 LEU CB B mod.= 2.446 id.= 1.530 dev= -0.916
>> sig.= 0.020
>> A 6 LEU CB A - A 6 LEU HB2 A mod.= 0.969 id.= 1.521 dev= 0.552
>> sig.= 0.020
>> A
>>
>> Rfree goes form 17 to 28 and R from 15 to 25.
>> Coot map looks like a bunch of busted insect parts.
>>
>>
>> I use the exact same input using ccp4 6.1.13 and Refmac 5.5 and all is good.
>> I am forced to use 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
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
inion on the idea of the depositions of the raw
> data, please vote here
>
> http://tinyurl.com/3qlwwsh
>
> I'll post the results as soon as they look settled.
>
> Cheers,
>
> Ed.
>
> --
> "Hurry up before we all come back to our senses!"
>
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
>> m
you for bringing peace to our home.
>> Julian, King of Lemurs
>
> --
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: + 44 1223 336500
> Wellcome Trust/MRC Building
-------
>> Francis E. Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder
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
in 79/80
>
> 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:
>>
>&g
79 5.2034 22.2151 1.4379 0.2536 1.5863 56.1720
> 0.8669
> ZN 14.0743 3.2655 7.0318 0.2333 5.1625 10.3163 2.4100 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
aw intensity mtz file or
> the newly 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
ran 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 Biolog
newest pdb requiring centered residue 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.
>
>
>
> ---
thing specific to my setup?
>>
>> Cheers,
>>
>> Ed.
>>
>> --
>> After much deep 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
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
e unlimited
>> filesize unlimited
>> datasize unlimited
>> stacksize8192 kbytes
>> coredumpsize 0 kbytes
>> memoryuseunlimited
>> vmemoryuse unlimited
>> descriptors 1024
>> memorylocked 64 kbytes
>> maxproc unlimited
&g
ank 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 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
ich number reported in the log-file)?
>>
>> Thanks for everyone's opinion and experience,
>>
>> Tim
>>
>>>
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID
im Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.11 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>
> iD8DBQFOVR
MacCHESS, Cornell University
> schul...@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
in a separate file *.tls or *.tlsin.
>
>Ethan
>
>
>
>> I dont see a place for entering a manual selection, eg resname FMN...
>> Thank you
>>
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
LINKR SER A 246 GLY A 248 gap Many thanks for your timeBest regardsAfshan
Garib N Murshudov Structural Studies DivisionMRC Laboratory of Molecular BiologyHills Road Cambridge CB2 0QH UKEmail: garib@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
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 interatomi
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 it
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
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 avoid
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, pa
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 for
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 # use this bvalue for sharpening with automatic
regularisation parameter
mapc sharpen alpha # sharpen with regularisation paramete
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 r
) and now I am 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 coul
degree of twinning) and now I am 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%
>> (
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 and there is no pseudo rotation parallel to twin operator.
Hypothetical case it can happen if you have refined one crystal structure at
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 tha
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 p
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 hav
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
www.ysbl.york.ac.uk/refmac/refmac_experimental/refmac5.6_linux.ta
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 s
> Is my case "translational disorder" as you said?
> If so, how can I solve it?
>
>
> Yours truly,
>
> K. Yamashita
>
> 2010/12/9 Garib N Murshudov :
>> In refmac you can remove vdw interactions between chains using the following
>> command
>>
>
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 Yama
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