Hello Niu,
Do you have pseudo translation. It could echo of another molecule that might be
in correct orientation.
Regards
Garib
On 14 Nov 2013, at 22:47, Phil Jeffrey pjeff...@princeton.edu wrote:
Hello Niu,
1. We need extra information. What program did you use ? What's the
If there is a covalent link between CYS and UNK then it is better to create
that using jligand from ccp4.
There are nice tutorials designed by Andrey Lebedev. Tutorials are on this site:
http://www.ysbl.york.ac.uk/mxstat/JLigand/
Regards
Garib
On 5 Feb 2014, at 15:59, Ronnie
Hi Ian
dod you try without link and standard ACE atom naming. Refmac should be able to
deal N-terminal activation and few other things. At least it was the intention
when it was written. Bugs may have been (self)introduced to prevent this from
happening. If it is so then I would like to know.
Dear Uli,
It seems that you are dealing with psued-twinning when cell do not overlap
after rotation with twin operator. In these case what is in one resolution on
one of the orientation becomes another resolution in another orientation of
crystals
In short:. You have an operator R that
There re two places where FSHANN is set. One when keyword is read and
one default initial value. The second value is the default.
The first set is when you make mistake with the keyword and the
second one is the default. Is this what you have?
When there are riding hydrogens then refmac gives rmsd for them
seperately (like rmsd for others. That is atoms not included in
refinement)
Garib
On 14 Mar 2007, at 17:02, Edwin Pozharski wrote:
Does anyone know if Refmac includes riding hydrogens in rmsd
calculation? Because if it
Chiralities in refmac dictionaries are local just like in smile
strings. You can of course put atoms by their priorities then
you will have correspondence to R/S assignments. However you do not
have to do it.
In many case I find it useful to put chirality 'both' and then refine
against this
I think your pdb header has cis conformation fnormation. Remove them
from the pdb header then it should work. If not, please let me know.
Garib
On 31 Mar 2007, at 22:16, Todd Holyoak wrote:
All,
We are currently refining a 1.6A structure with Refmac5. There are a
few loops with backbone
It looks like a bug. Insertion code should have been used in NCS
restraint definitions. It seems it does not. I will try to fix
it asap.
Insertions are usually no problem. Problems arise when you have
deletions (i.e. residue numbering is
not sequential). Then you need to use LINK record with
You just put on the element column of pdb MG+2 instead of MG (you can
do it on the atom name column also but if you have the element column
then that will
be used to interpret element name with its oxidation state)
Garib
On 9 May 2007, at 13:41, Dirk Kostrewa wrote:
Dear CCP4ers,
I try
Dear all,
A new version of an automatic molecular pipeline system - BALBES is
now available.
It can be downloaded from: www.ysbl.york.ac.uk/~fei/balbes
The new options in this system are:
1) Use of user defined external PDB library
2) Use of a single PDB file as an input model for Molecular
Residue name of iodine should IOD. Otherwsie there is a clash of
names with some other residue names (ionisine)
Garib
On 6 Jun 2007, at 16:56, [EMAIL PROTECTED]
wrote:
Dear All,
I am having trouble with refmac dictionaries when refining a
structure that contains an iodine ion.
the PDB
It looks like as if your PDB is corrupt. For example there atoms B
that should not be present inamino acids.
Garib
On 9 Jul 2007, at 19:55, JINJIN ZHANG wrote:
Hello all,
I'm working on a protein-DNA complex. My protein is a trimer and
the crystal has 3 trimers in an AU. I used a pdb
It would help if you would also show surrounding atoms.
Garib
On 26 Jul 2007, at 23:10, Wu, Mousheng wrote:
Here is the extra density map in my structure. It is too big for
glycerol although I used glycerol as cryoprotectant.
Thanks for your quick responses.
Mousheng
density.TIF
I the previous mail when announcing webserver I forgot to give web
address.
Here is the web address of our server. Please use and let us know
your suggestions.
http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
with best regards
Garib
Dear all
We are pleased to announce the first version of our web server. You
need to register to use it. That is our university's security policy
we have to be in line with.
Current version of the server has two runnable programs:
1) BALBES - completely automatic molecular replacement
If you are dealing with phosphoserine then there is a monomer called
SEP that is phosphorilated serine. pdb coordinates are attached:
regards
Garib
libcheck_SEP.pdb
Description: Binary data
On 4 Sep 2007, at 23:41, U Sam wrote:
Hi
I am trying fit a ligand (organo phosphate) covalently
Number of electrons are rarely (if ever) used. In principle sum of
the coefficients of gaussians should be equal to the number of
electrons.
Ions from nonions are distinguished by just addition charge on the
element column. Example:
ATOM 4175 CLCL I 1 5.299 23.521 60.812
In the previous email I missed index.jsp. Here is the correct url for
programs (including molrep). So again
In newer version of molrep cubic space groups are handled much
faster. Here is the url where you can download molrep
http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
regards
Garib
Others: Atom not included in refinement. If at least one of the atoms
not included in X-ray grad and secder calculation they are marked as
others. These are usually
hydrogens.
Period means if torsion angle has one, two, three or four minimums.
Garib
On 4 Nov 2007, at 20:56, Flip
In principle in refmac you can resrtraint any torsion angle you want.
If this torsion angle has definition in the dictionary. It includes
phi/psi also.
See
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html
For example for phi you can do (phi is the proeprty of link between
There is nothing to worry about this message. I just means that some
of your B values may be too large.
It does not affect refinement as far as I remember.
Garib
On 19 Nov 2007, at 21:13, mark Mayer wrote:
Hello,
I'm running a TLS refinement with Refmac and keep getting the
following
But you can change it with the keyword
anomolous formfactor element f' f''
Where f' and f'' correspond to values for a given wavelength.
See for details:
http://www.ysbl.york.ac.uk/refmac/data/refmac_news.html
Internally yes. It is CuKa.
Garib
On 29 Nov 2007, at 23:19, Tadeusz Skarzynski
Weights are the same. 5.4 has a lot of small bug fixes and
performance enhancement and some added stability things.
And some new features I am planning to announce soon.
Since I am responsible, my extremely biased view is that 5.4 is better.
Garib
On 5 Dec 2007, at 13:05, Jianghai Zhu
This result means that you need to use TLS refinement and it may
improve your statistics considerable.
Garib
On 6 Dec 2007, at 11:27, Ronan Keegan wrote:
From: Rafael Couñago [EMAIL PROTECTED]
Date: 6 December 2007 04:58:51 GMT
To: [EMAIL PROTECTED]
Subject: [ccp4]: iso - anisotropic B
Hi Mark
I used to do followings: Run 0 cycle of refmac with aniso refinement
and then take aniso cards for atoms I want to refine aniso and put in
the relevant position of the
original pdb file. After that I would do mixed refinement.
I should warn that I have not tested this option for a
Dear all
New version of refmac (stable version 5.4) is now available.
Apart from bug fixes and stabilization it has some features include:
refmac:
(see for description of some of the keywords in this version: http://
www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html)
1) f' can be given
noticed this line in the log file:
Before the second run
Unknown atom for fprime and f2prime calculation
I didn't receive this error in the older version. Please explain.
I'm only specifying f' and f'' for the Selenium.
Thanks,
Mark
On Jan 1, 2008, at 10:29 AM, Garib Murshudov
On 2 Jan 2008, at 17:15, Ethan Merritt wrote:
On Tuesday 01 January 2008 06:40, Mark A Saper wrote:
Well, I guess one shouldn't change versions of refmac in the middle
of a structure refinement. What are the major differences between .
0034 and .0066 ? I noted that form factors for the Se
lying around on my disks
all contain the correct value.
Ethan
Just curious.
Regards,
Boaz
- Original Message -
From: Garib Murshudov [EMAIL PROTECTED]
Date: Wednesday, January 2, 2008 19:19
Subject: Re: [ccp4bb] Refmac 5.4.0066 versus Refmac 5.4.0034
Best way of refining SO4 two-fold axis is to put al occupancies equal
to 0.5 and refine like that.
You may need to use newer version to deal better with atoms in
special position. Have a look:
www.ysbl.york.ac.uk/YSBLprograms/index.jsp
You can go from this site to latest refmac site.
Any
sorry for repeat. Link I gave in the previous mail should be:
www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
Garib
On 11 Jan 2008, at 19:58, Jie Liu wrote:
I've played around for a while, also read the manual
and googled the internet, but just couldn't find a way
to set up the restraints to the
Dear Catherine
Is your SUU an amino acid modified on the side chain side? If yes
then you can use standard peptide links. For this your SUU should be
declared as L-peptide in the description. Can you send description of
your SUU and I can try to sort out what is going on.
Garib
On 26
(In my
view of course, which is debatable)
Garib
On 4 Apr 2008, at 06:56, Frank von Delft wrote:
Is that also how you would restrain refinement at low resolution
when using a high-resolution model? (e.g. a 1.8A model into 4A data)
phx.
Garib Murshudov wrote:
In newer version of refmac
Dear all
After announcing molecular replacement server with all allowed space
group checks because of rapid increase of the usage our system could
not handle it and we had to turn off this option.
Now we have upgraded the system and it is ready for to use.
Note that the new option of the
If you are using new version of refmac from
www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
then you can use harmonic restraints. Have a look for instructions:
www.ysbl.york.ac.uk/refmac/data/refmac_news.html
I hope it helps.
regards
Garib
On 6 May 2008, at 16:39, Debasish Chattopadhyay wrote:
It will be available tomorrow (hopefully) afternoon.
Garib
On 19 May 2008, at 19:50, Thomas J Magliery PhD wrote:
I am trying to upgrade Refmac from 5.2 to 5.4. I didn't download
the monomer library (refmac5.4_dictonary.tar.gz) when I downloaded
the executables, and I can't access the
On 23 May 2008, at 02:03, Bernhard Rupp wrote:
Dear All,
I have a 3 minor questions re refmac internals:
1) does refmac use angle values directly or restrain 1-3
distances for angle restraint setup?
Yes. Angles are angles in degrees.
2) the ML coefficients FWT and DELFWT - are they the
Dear all
New version of refmac (v 5.5) is now available for use. Please have a
look:
www.ysbl.york.ac.uk/refmac/latest_refmac.html
Major new developments are:
1) Maximum likelihood refinement against data from twinned
crystals. Current version allows only one instruction: twin
All
it was there for some time. Info about this and some other new and
not so new features can be found here:
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html
Some of the features like n mfo-l dfc map was there for 5.3 and may
be even earlier.
regards
Garib
On 8 Jul 2008,
Dear Snageetha
1) Could you check please if specified atoms have zero occupancy.
Atoms with zero occupancy are considered as absent and there are not
restraints on them
2) symm y at the end of instructions means that the program check all
possible symmetry operators and finds minimal
[mailto:[EMAIL PROTECTED] On Behalf
Of Garib Murshudov
Sent: Wednesday, July 30, 2008 5:18 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Preventing close contact between protein and
ligand
Dear Snageetha
1) Could you check please if specified atoms have zero occupancy.
Atoms with zero
There should be something like:
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
MAN-b-D O1 C1single 1.4100.020
MAN-b-D C2 C1single 1.524
in order to have the well behaving refinement I
will have to change these occupancies to 50-50, right? And just pay
the price with the higher B factors? Or is there any other way to
deal with this situation?
Aleks
On 30 Jul 2008, at 16:15, Garib Murshudov wrote:
If sum of occupancies of atoms
Hi all
One should be aware of some stats about twinning (and in general):
1) If you have perfect hemihedral twinning and no correlated
rotational NCS then random R factors are around 40 instead of
Luzzati's 58.
2) If you have perfecthemihedral twinning and you are not modelling
twin then
development team:
Fei Long, Paul Young, Andrey Lebedev, Alexei Vagin and Garib Murshudov
in collaboration with ARP/wARP development teams in Hamburg and
Amsterdam
Garib Murshudov
http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
Erice 2010: Structure and Function from Macromolecular
/ *
**
*
Garib Murshudov
http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
Erice 2010: Structure and Function from Macromolecular
Crystallography: Organization in Space and Time
http://www.crystalerice.org/erice2010/2010.htm
Garib Murshudov
http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
Erice 2010: Structure and Function from Macromolecular
Crystallography: Organization in Space and Time
http://www.crystalerice.org/erice2010/2010.htm
Dear All
Happy new year to you all!!
JLigand is a java application which allows ligands to be linked on-
screen and a link description to be created.
JLigand 0.1 Beta is now available at
http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html
There is a documentation how to use JLigand
If top/par file could be converted to the following type of
instructions then you do not need to define everything in cif file
(these are for torsion angles, all other restraints can be defined
similarly)
General torsion angle restraints for any quartet of atoms:
external torsion first
Dear Nick
Using TLS sometimes improves behaviour of NCS restraints (it makes
sense since remaining B values should be similar). However in other
cases it does not improve. Perhaps removal of B value restraints for
these domains may improve NCS restrained refinement. I have not done
tests
IT could be miscommunication between refmac and coot. Try to remove
cispep lines from your pdb and refine again. Then it may work. After
model building info about cispep and/or ssbridge should be removed
from the pdb file (unless you are confident about them)
regards
Garib
On 25 Jan 2009,
There is an option to do harmonic restraints:
external harmonic chain [ch] residue [res] insertion [ins] atom [n]
[altcode [a]] [sigma [value]]
or
external harmonic residues from [residue_number] [chain_name] to
[residue_number] [chain_name] sigma [value] sigma 0.1
For example:
Child killing and/or wrong bus seems to be related with static
compilation on Mac intel OS 10.5. Existence of this bug is the reason
why the version with bug fixes was not announced.
If you build from source code then this bug can be overcomed
Download source files and copy them to ccp4
Dear Gerard and all MX crystallographers
As I see there are two problems.
1) Minor problem: Sanity, semantic and other checks for currently
available data. It should not be difficult to do. Things like I/sigma,
some statistical analysis expected vs observed statistical behaviour
should
Current version does not expand data or model. C222 twinned in P2 will
not be handled if data are in C222.
Overmerged data are a bit tricky to deal with. And model in higher
space group would not fit into the asymmetric unit in general.
In short: in the current version space group should be
As far as I know map coeffiicient correspond to detwinned data. But
using detwinned data may not be a good idea.
It would be good to see what are R factor. Another thing to consider
is that different program may use different flags for free R and it
may cause some problem.
What are Rfactors,
On 18 Mar 2009, at 01:47, Bernhard Rupp wrote:
I mean *absent* reflections here with fobs=0
Dear All,
during processing some mtz files I noted that some programs complete
the reflection list by padding missing reflections.
a) for Refmac (which did not pad
Dear all
Before going into and trying to find a technical solution to the
problem it would be good if decide if we need images. As far as I know
if we face with a problem to solve and we know that it is necessary to
solve then we find technical solution to the problem (either from
other
Perhaps you could try to use JLigand. It may do a better job. it is
available from:
www.ysbl.york.ac.uk/mxstat/
In the jligand session there are two tutorials also. they may help you
to run and generate your ligand description.
If any problem please let me know.
In general refmac is not
In the latest, latest version refmac writes LINK instead of LINKR. It
is a temporary solution. We need a better solution and hopefully we
will have one soon
This version of refmac is available from:
www.ysbl.york.ac.uk/refmac/data/refmac_experimental/
regards
Garib
P.S. This version also
I guess you are using version 5.5. In that version in the beginning
the program finds all possible twin operators and assigns twin
fraction for each of them. Then it tries to filter out smaller twin
domains and takes only significant domains. I.e. when twin fractions
are higher than 0.05
Prodrg does very good job in guessing atom types and bond orders. Once
it guessed things right it does extremely good job in generating bond
lengths, angles etc.
But it still depends on accuracy of coordinates. You need to check
carefully bonding orders before using them in refinement.
You
In your run with the option residues are close only refmac also
should generate a pdb file with link records added. In very simple
form you can edit this pdb file and remove all unnecessary links and
leave link you want. Then you can rerun with normal options and
generated library.
Better
There may be several reasons:
It looks strange. Something seems to be wrong in protocols
1) Check free R flags. I have seen in few cases wrong free R.
Generally number of reflections for free should be less than for work
reflections
2) Check TLS refinement. You may need to restart TLS
Better link with nice tutorial from Andrey is:
www.ysbl.york.ac.uk/mxstat/
In the JLigand section there are some tutorials from Andrey to
demonstrate how covalent links can be generated and used.
Garib
On 14 Jul 2010, at 14:35, Paul Emsley wrote:
On 14/07/10 12:56, Vandana Kukshal wrote:
You can use harmonic restraint. There is no option on the interface.
However you can create and use keyword file on the interface.
In the keywords file you need to give instruction where you want to
put harmonic restraints. Syntax is:
for particular atom:
external harmonic chain [ch]
Hi
As far as I know Paul and Eugene are working very hard to make this
option painlessly available to users. With the current versions of
refmac and coot I would check carefully at every stage. In coot I
would look at the distance berween atoms supposed to be linked (even
if they are not
I would be careful with Rfactors at the early stages of refinement,
especially in the presence of twinning (apparent or real). You can see
weird behaviour of Rfactors in this presentation:
www.ysbl.york.ac.uk/refmac/Presentations/Refmac_Erice_workshop.ppt,
slides 18-20.
In short if you
Are you suggesting ccp4 is collapsing and people are coming back to
the original source?
Garib
On 25 Aug 2010, at 22:17, Pavel Afonine wrote:
On 8/25/10 2:11 PM, George M. Sheldrick wrote:
I would like to propose that we rename this list to the Phenix (and
CCP4) Bulletin Board.
Sounds
Why you do not use coot? It does exactly what you want.
regards
Garib
On 25 Aug 2010, at 22:33, Hailiang Zhang wrote:
Hi,
Can some utilities of CCP4 do the real-space refinement locally
with the
residue range explicitly specified?
By the way, I have registered phenix bb. Just didn't
I think Paul (Emsley) is better qualified to answer to this question.
However 1) coot uses 2mFo-DFc maps 2) you should be able to feed any
map you want to coot so it is nice place for experimenting this kind
of calculation 3) You may try to relax gemetry 4) Usually if the
model does not
But equation given in slide #4 is exactly least-square equation with
some modified maps. Just use Pareval's theorem, then for case of 2mFo-
Dfc you will have
sum_{reflection used) (2mFo-DF_{c current) -k F_{model})^2
F_model is equal to F_{c current} at the point of calculation. All
This case would happen if the program first decides that the number of
twin operators are several. But them to be twin cell should be
deformed. This deformation makes some of the reflections to be
equivalent to higher resolution reflections than they are.
After calculating Rmerge and twin
It is in general matter for debate what to do in these extreme cases.
When NCS rotation is parallel to the potential twin operator even if
twin is present electron density does not change much (at least not as
much as we would like). There are many cases where because of this
twinning was
or suggestions please do not hesitate to
contact with one of us. Your suggestions, complains and questions were
instrumental in developing this system.
Fei Long - f...@ysbl.york.ac.uk
Alexei Vagin - ale...@ysbl.york.ac.uk
Garib Murshudov - ga...@ysbl.york.ac.uk
regards
Garib
Dear all
Since last announcement the number of usage of YSBL server was more
than our server could cope. That is why we had to close it for few
days and upgrade the sfotware on the server. Now YSBL programs server
is open again and it should be able to cope (at least for a while).
All
...@jiscmail.ac.uk [mailto:owner-
ccp...@jiscmail.ac.uk]
On
Behalf Of Garib Murshudov
Sent: 16 August 2009 22:09
To: Tim Fenn
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] LINKR in refmac
Tim is right. The link you want is TRANS. And if you want link
between
alternative position then you need
You may try Andrey Lebedev's Zanuda program from
www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
If the problem is related due to false origin related with the
presence of strong pseudo-translation then this program may be able to
sort this out. In some cases it may also correct space group (if
Same goes for refmac 5.6 series. It should be stable enough for
general use in a few months time
Garib
On 2 Oct 2009, at 14:10, harry powell wrote:
Hi
I'd like to point out that anyone trying to do anything with Mosflm
7.0.6 does so at their own risk - I don't anticipate it being
Dear RajeshCould you please try the attached dictionary. Please let me know if it still has a problem.What are the issues around O1N-PN-O2n and O3N-PN-O5?regardsGarib
nad_exp.cif
Description: Binary data
On 8 Oct 2009, at 15:11, RK Singh wrote:Dear All,I would like to request to send me a working
You can try JLigand from
http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html
to create link and then add link record on your pdb
Garib
On 9 Oct 2009, at 03:40, Sampath Natarajan wrote:
Dear All,
I’m currently refining the structure (2.0 A) with a cofactor PLP.
The PLP density is
Few people had complains about this. It seems to be related with
compilation. If you take the version from York's website then it
should work fine.
www.ysbl.york.ac.uk/refmac/latest_refmac.html
I have compiled it for mac 10.5 and it does not seem to work on mac
10.4. I am trying to make
Could you please try the version from York:
www.ysbl.york.ac.uk/refmac/latest_refmac.html
I think probkem you mention is related with compilation or something.
At least I cannot repat it on my computer
regards
Garib
On 25 Nov 2009, at 16:18, John Pascal wrote:
Hello All,
We are trying
What are the versions of refmac you are using.
Differences (as Pavel mentioned) could be scaling and different
scaling parameters.
If you would send your log file to me I can try to find out and try to
sort out this problem.
regards
Garib
On 4 Jan 2010, at 17:35, Feng Guo wrote:
Hi,
I
I thought this problem is fixed. Could you please try the version from:
www.ysbl.york.ac.uk/refmac/latest_refmac.html
Problem was that when refmac starts twinning analysis it uses generous
tolerance and then filters out unlikely twin operators.
When large deformation is needed merohedral
Can you check your input file. It may contain contain link record
already
regards
Garib
On 1 Feb 2010, at 13:52, Jan Dohnalek wrote:
Dear all
I understand that when I use the Refmac keyword
make link no
Refmac should not apply found links.
It keeps finding links between ligands (Na+ and
If you want dictionary, atom naming and everything else about new
compound names you can copy all monomers (in our definition) from:
ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/monomers/components.cif.gz
It has all compounds used in pdb with idealised coordinates,
compound
One option would be molrep
molrep -m model1 -mx model2
Of course it assumes that your two structures have overall similar
structures and no substantial conformational changes.
As the question posed, I think, it does not have solution (only
approximations). Almost all programs assume
Hi
Waters are not restrained in any case. There are only antibumping
restraints for waters. If you want to remove them then please let me
know and I will send you instructions how to do it.
If you want to remove (or relax) restraints from ligand you need to
edit your dictionary for this
It is part of the new dictionary we are preparing. Please find
attached dictionary. It was not in the distributed dictionary.
Garib
CAQ.cif
Description: Binary data
On 2 Apr 2010, at 22:53, Vin Purp wrote:
Does anyone know what happened to the monomer CAQ? There are several
structures
As I see there is no chirality definition for NAG-ASN link (perhaps
there should be but then people will be unhappy even more).
Only reason i can see for this flattening is conflict between geometry
and electron density. Your example shows that even if electron density
is weak it may play a
. Here you have only two orientations.
Garib
On 21 Apr 2010, at 14:20, Paul Emsley wrote:
Garib Murshudov wrote:
As I see there is no chirality definition for NAG-ASN link
(perhaps there should be but then people will be unhappy even more).
Only reason i can see for this flattening is conflict
You may be using output reflection data from the previous cycle of
refinement for the next session. After twin refinement output Fobs
(confusingly) may be detwinned. You can try to use original reflection
data file (e.g. after scala/truncate/freerflag) and for refinement
and it may
And another (not so) minor point: Defferences between R/Rfree with
twin on and off suggest that there is strong correlation between twin
and NCS. For this cases better dealt with if you use twin refinement
with sufficiently strong NCS restraints. In new refmac (www.ysbl.york.ac.uk/refmac/
I hope Kevin will respond soon. I think he has done (or is planning to
do) to twinning and ncs in his pipeline of model building.
I think something like that may already be in new ARP/wARP (Victor and
Tasos will correct me if I am wrong)
regards
Garib
On 23 Apr 2010, at 23:16, Ethan Merritt
I am getting in habit of writing double emails.
I would say that refmac overestimates at early stages and truncate
underestimates (it is just an intuition, not based on theoretical or
empriical results)
Garib
On 23 Apr 2010, at 23:16, Ethan Merritt wrote:
In a nutshell
=
I think your procedure is good with current technology. At early
stages twin refinement may give misleading results.
An intuitive resoning for low R factor would be: Twin is summation of
intensities. As you sum intensities two things happen: 1) distribution
of intensities become more
Thank you, Frank, for pointing this out
Here is the link to that presentation again:
www.ysbl.york.ac.uk/refmac/Presentations/Refmac_February.ppt
Garib
On 24 Apr 2010, at 12:05, Frank von Delft wrote:
Hi Garib, the link you sent doesn't work from here,
phx.
On 24/04/2010 00:17, Garib
Hi Remie,
You can add harmonic restraints for parts you do not want to move too much.
Instructions could be found here:
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html#Harmonic
Regards
Garib
On 13 Aug 2014, at 15:44, Remie Fawaz-Touma remiefa...@gmail.com
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