Hi Tim,
There is an option to do unit cell parameter refinement (for all six parameters
in general which can only happen in P1). It is undocumented.
Celrefine/lattice refine all # if you give scale instead of all then only one
parameter is refined.
Cellrefine select . # use only atomic B val
Garib
> On 16 Jul 2020, at 22:34, Garib Murshudov wrote:
>
> Hi Tim,
>
> There is an option to do unit cell parameter refinement (for all six
> parameters in general which can only happen in P1). It is undocumented.
>
> Celrefine/lattice refine all # if you give scale
n quite stable, and the distance can vary by about 5%...
>
> Best regards,
> Tim
>
> On Thu, 16 Jul 2020 23:21:54 +0100
> Garib Murshudov mailto:ga...@mrc-lmb.cam.ac.uk>>
> wrote:
>
>> One correction: Model should after molecular replacement and few
>>
Hi Robbie and Eleanor
There are links for Zn-His and Zn-Cys. They meant to be used automatically,
obviously something is not entirely right.
Link names are:
ZN-CYS
It has a bond between Zn and S as well as an angle:
ZN-CYS 1 ZN 2 SG 2 CB 109.0003.000
This also removes H
1.00 13.12
> Z 403 ZN B Z 601 O4 B 1.938 X,Y,Z 0.70 14.10
> Z 403 ZN B O 825 OC 2.322 X,Y,Z 0.20 10.61
> ~
>
>
> On Tue
residues. For general solution we need a bit different approach (e.g.
coordination analysis).
Regards
Garib
>
> Jan
>
>
> On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov <mailto:ga...@mrc-lmb.cam.ac.uk>> wrote:
> What are these numbers?
>
> If I understand t
ures restraining the coordination geometry
> is not necessary, they hold nice.
>
> Jan
>
>>
>> Jan
>>
>>
>> On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov > <mailto:ga...@mrc-lmb.cam.ac.uk>> wrote:
>> What are these numbers?
>>
nt? all difficult at low resolution..
>
> On Tue, 8 Sep 2020 at 20:29, Garib Murshudov <mailto:ga...@mrc-lmb.cam.ac.uk>> wrote:
> Hi Jan,
>
>
> It is my experience also that if atoms are in more or less correct positions
> then non-bonding interaction together ke
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 to
Hi Ed
Negative and 0 Fobs are not allowed and they are removed from
consideration and flagged as unmeasured in the current version.
However you can have negative I (if you are using intensities in TWIN
mode). If you are using this after sampling the perhaps sampling
should be done using i
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 ha
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 twinn
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 liga
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 -mx
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 either atom labe
Automatically yes. But you can force it to use only one conformation.
You need to use link record instead of ssbond (they are essentially
same). To do this you need to put link records just before cryst1
card. Examples of link record are in:
http://www.ysbl.york.ac.uk/refmac/data/template_l
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 lig
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 i
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 r
amers. 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 con
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 clarif
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
=
Is
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 symmet
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,
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 th
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 c
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 refinem
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] residue
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 have
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 reali
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 fit
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
gradien
Dear all,
It is an announcement of a beta-release of an automatic molecular
replacement system - BALBES.
It is available from: www.ysbl.york.ac.uk/~fei/balbes
There are tar files for Linux, MacOS (G4/G5) and MacOS (intel).
There are instructions how to install and use the system.
The system
Dear Jeremiah
B values on individual atoms is only residual B value and do not take
into account TLS contribution. If you want to have full B value
then you can use TLSANL.
Regards
Garib
On 6 Feb 2007, at 21:48, JEREMIAH R WAGNER wrote:
Hello All,
Our group is having discussion about B v
Dear Carlos
When you add hydrogens in refmac they are used in geometry and
structure factor calculations. They are not used in refinement fully.
I.e. their contribution
is taken into account and but they do not contribute to gradients and
hessian.
regards
Garib
On 12 Feb 2007, at 03:42,
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?
/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/
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 does,
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 d
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 ge
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 to
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 r
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
I- ?? or have I misunderstood horribly ?
J
--
Dr Judith Murray-Rust
Structural Biology Lab
Cancer Research UK
London WC2A 3PX
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On
Behalf Of Garib Murshudov
Sent: 06 June 2007 17:14
To: CCP4BB
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 fi
1) Rfree in the first cycle seem to be more apparent than actual. You
need to check you free reflection conversion. It may turn out that you
have more reflections for free than for working R.
2) You may need to use tighter restraints. For example by changing
weight matrix value to smaller numb
Current version of refmac will not allow you to extend resolution.
there are more problems that need to be solved before proper
resolution extension
implemented
Garib
On 14 Jul 2007, at 22:37, JOE CRYSTAL wrote:
Dear all,
I am refining a structure in Refmac at 2.3 A and I set resolution
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
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 pi
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 bon
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
Dear Jacob
The main reason why different programs produce different resutls is
that methods used in these programs are different.
For example refinement programs use different methods for scaling.
Some include bulk solvent a Babinet, some use
mask bulk slvent and some use anisotropic scaling
I think it is now much faster. If you take the version from Alexei's
home page it should be faster and may be better also.
You should be able download it from this site:
http://www.ysbl.york.ac.uk/YSBLPrograms
Garib
On 17 Sep 2007, at 10:10, Manfred S. Weiss wrote:
Dear CCP4ers,
has anybod
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 Hoedemaeke
I could not say about other program but in refmac there are intra
residue vdw repulsions if atoms are at least two bonds are apart.
If atoms are only two bonds apart then vdw distance is reduced and it
can be controlled.
I do agree that at lower resolution you should use as much info as
you
I am for it also. It is a god idea!!
Garib
On 9 Nov 2007, at 13:56, Ian Tickle wrote:
I like it!
-- Ian
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Eleanor Dodson
Sent: 09 November 2007 13:51
To: Phil Evans
Cc: CCP4BB@jiscmail.ac.uk
Subject: R
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
amin
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 outp
But you can change it with the keyword
anomolous formfactor 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 wrote:
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 wrote:
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
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 Yogesh
Could you please try the version from York
www.ysbl.york.ac.uk/refmac/latest_refmac.html
You need to take appropriate refmac 5.4 (it is current stable
version) and dictionary. I remember that in older version there was a
problem in one of RNA bases and it has now
been corrected
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
xtra-param" file.
2. In version 5.4.0066 version I 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
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 at
Try the version 5.4
www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
We have fixed this and some other irregular behaviours
Garib
On 2 Jan 2008, at 21:42, Roni Gordon wrote:
Hi all,
I observed a very strange phenomenon with a high-resolution dataset
phased via rigid-body refinement (using the apo
If you take new dictionary with new refmac it may solve this and some
other naming problems.
Try from the website:
www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
Garib
On 3 Jan 2008, at 16:53, Daouda TRAORE wrote:
Hi all,
I'm trying to refine a protein DNA complex using Refmac.
Unfortunately t
(') instead of asterisk (*) for the
ribose
numberings, and uses OP1 instead of O1P, and so forth.
Do the new refmac dictionaries have that (I haven't been able to
get it to
work in the context of coot).
Garib Murshudov wrote:
If you take new dictionary with new refmac it may solve thi
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
To:
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 fur
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 s
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 Feb
make sure that you are using the original observation (Fobs and
corresponding sigmas) not that produced by density modification (e.g.
solve resolve) programs.
Garib
On 28 Mar 2008, at 10:43, stefano ricagno wrote:
Dear CCP4bb readers,
this is my problem:
I solved a structure by MR: the sol
In newer version of refmac you can use harmonic restraints.
Take the new stable version of refmac from
www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
and use harmonic restraints as described in:
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html
Keyword is:
external harmonic residues f
(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
The new version of BALBES webserver is now available.
Since the first firs release (July 2007) a lot of bugs have been
removed.
The major new option of the server is to check all potential space
groups.
The system runs the full molecular replacement for all potential
models and the
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 ser
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 Refm
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 com
I think in refmac it has already been fixed (since October or so).
refmac 5.4 and later version should handle all available space groups
with their various disguises.
Garib
On 10 Jun 2008, at 16:11, Clemens Grimm wrote:
seems to be a 'non-standard' setting. Refmac also has problems with
th
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 dec
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, at
You may need to consider (assuming that space group is correct)
1) Twinning. In this case even wrong solution at the early stages
would give lower Rfactor and at the later stages higher Rfactor
without accounting for twinning
2) Pseudo translation. In this case the solution could be in wrong
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 distan
[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
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 r
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