On Fri, 2011-06-10 at 12:48 -0700, Ethan Merritt wrote:
I don't think that combination makes any sense. Whatever anisotropic
is being described by the TLS parameters can also be fully described
by the individual anisotropic U^ij terms. So the TLS parameters are
entirely redundant, leading
Hi Ethan,
I also reset the temperature factors to 20 at
the beginning of each refinement round. The refinement resolution is 75
to 1.8 A, and the space group is C2, if it matters.
I am virtually certain that refinement of individual anisotropic
U^ij terms cannot be justified at 1.8A.
I've split this off from the too many clashes thread as it's not directly
related.
I was under the impression that the default in refmac was to add riding
hydrogens but some investigation suggests this may be only appear to be the
case.
If the default option in the CCP4i GUI for refmac with
Dear all,
I might excuse myself for the silly question but it is the first time I
solve an x-ray structure.
After modell building in coot and running of refmac with restrained
refinement I have the problem that the pdb output file contains
distances between e.g. ILE Cb and Cg that are so long
Well - REFMAC and I think other refinement programs simply read in an
atom with occupancy 0.00 and write it out again in exactly the same
place.. All refinement contributions for atoms both Xray and geometrical
are weighted by the atom occupancy so such an atom will not shift.
The assumption
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
Marcus,
it appears that coot breaks bonds when the distance between atoms
exceeds 1.64A pretty much irrespective of the bond type. Two exceptions
are, of course, sulfurs in MET/CYS. CB-SG bond in cysteine does not
seem to have any cutoff (when you do rotate/translate zone in coot, you
can move
I think it would be a lot easier to understand what's going on if you
posted your actual scripts.
Cheers
-- Ian
On Mon, Dec 20, 2010 at 6:11 PM, zhan...@umbc.edu wrote:
Thanks Ian, but I was using the output from 2a for 2b running. Results are
still different between 2 and 1. More curious is
On Sun, 2010-12-19 at 18:58 -0500, Hailiang Zhang wrote:
(1). CTLS=a, CC=b
(2). CTLS=a, CC=0; followed by: CTLS=0, CC=b
In (2), you are doing two separate runs, with the second not using TLS.
If you want to combine TLS and positional refinement, you must have them
included in the same refmac
I would try it with the latest version (5.6.x) in case there's a bug.
That's a very old version you're still using!
-- Ian
On Sun, Dec 19, 2010 at 11:58 PM, Hailiang Zhang zhan...@umbc.edu wrote:
Hi,
I am using REFMAC 5.2.0019 to run the following script:
***
refmac5 hklin a
PS one other thought: in your run 2b you are not reading in (as TLSIN)
the TLSOUT file produced by run 2a. So run 2b is not starting from
the same point that it would have done as in run 1.
I.
On Sun, Dec 19, 2010 at 11:58 PM, Hailiang Zhang zhan...@umbc.edu wrote:
Hi,
I am using REFMAC
...@gmail.com
Subject: Re: [ccp4bb] REFMAC 5.2.0019 question
To: CCP4BB@JISCMAIL.AC.UK
PS one other thought: in your run 2b you are not reading in (as TLSIN)
the TLSOUT file produced by run 2a. So run 2b is not starting from
the same point that it would have done as in run 1.
I.
On Sun, Dec 19
Thanks Ian, but I was using the output from 2a for 2b running. Results are
still different between 2 and 1. More curious is more second question, the
region with identical ADPs still ended up with identical ADPs (although
different from before running) after 1, and that's why I also tried 2.
On Mon, 2010-12-20 at 13:11 -0500, Hailiang Zhang wrote:
Thanks Ian, but I was using the output from 2a for 2b running.
It's not enough to use the pdb output - you have to make the proper tls
input file for refmac to incorporate the tls correction
--
I'd jump in myself, if I weren't so good at
Hi,
I am using REFMAC 5.2.0019 to run the following script:
***
refmac5 hklin a xyzin b eof
REFI TLSC ${CTLS}
REFI BREF OVERall
NCYC ${CC}
**
I thought this script will do CTLS cycles of TLS refinement followed by CC
cycles of verall B and geometry refinement. Then I did
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
Hi ,
i just tried the extra information because I had a serious overfitting of my
model. Roughly 10 % difference for 1.9 Ang. resolution and experimantal
phasing. I thought maybe the extra information and the adjustment of the
weighting parameters helps me to figure this out. A refinement
Dear all,
I want refine my model using TLS plus phase information from experimental
phases.
I used the TLSMD server to generate the initial tls parameters and started
Refmac
After an initial round of TLS refinement Refmac stops and and claims a problem
but nevertheless writes at the end Task
On Monday, October 11, 2010 11:01:10 am Christian Roth wrote:
Dear all,
I want refine my model using TLS plus phase information from experimental
phases.
I used the TLSMD server to generate the initial tls parameters and started
Refmac
I don't know exactly what has gone wrong.
Let's
On Monday, October 11, 2010 01:04:49 pm Christian Roth wrote:
Dear Ethan,
thanks for your fast answer. The pdb file does the trick. I also did not
click
the reset B-factor box, which I thought is equivalent to the TLS+Biso pdb. Is
that wrong?
For what you are doing, it is correct to
Hi Ethan,
So far as I know, there is still no provision in phenix for reading in
existing TLS parameters. It always wants to regenerate them for itself.
You are right, given suggested optimal selection for TLS groups
phenix.refine is capcabale to do the rest as good as it can. There is
Hello,
following this discussion, I was wondering how much sense it makes to use
TLS domains and experimental phases at the same time.
I would have thought that TLS domains are better to be used when the model is
fairly complete at which state the quality of the experimental phases are
probably
On Monday, October 11, 2010 12:31:13 pm Pavel Afonine wrote:
Hi Ethan,
So far as I know, there is still no provision in phenix for reading in
existing TLS parameters. It always wants to regenerate them for itself.
You are right, given suggested optimal selection for TLS groups
Hi Tim,
following this discussion, I was wondering how much sense it makes to use
TLS domains and experimental phases at the same time.
I guess both things are completely irrelevant. With using experimental
phases you bring in more data. And with using TLS you simply use a more
adequate
Hi Ethan,
yes, I must be missing something indeed...
You are missing the point.
What if you want to calculate Fcalc based on an existing model?
What if you want to explore application of the _same_ TLS model
to different sets of starting coordinates?
Yes, if I do need to calculate Fcalc
Hello Pavel,
thank you for the PDF file. When I search for the word phase starting from
page 24, all I find are phenix.phase_and_build and
phase_and_build_params.eff on p. 34, and they don't explain the problem.
I agree that experimental phases are data, but they might be utterly noisy data
and
Hi
I think you have very good point here. Towards the end of refinement (when TLS
refinement make more sense since the effects of positional coordinate errors on
B values become smaller) phased refinement refinement makes less sense
especially if phases are from density modification
following this discussion, I was wondering how much sense it makes to use
TLS domains and experimental phases at the same time.
My take on it is that if you have low resolution data, then it makes a
good deal of sense to use both experimental phases and TLS groups. But
this assumes that the
Of course if you have low resolution and good quality of phases then using
phases would improve the model (since model errors are going to be large in any
case). In this case it makes perfect sense to use TLS and phased refinement
simultaneously.
It will of course depend on resolution and the
Is it possible to use refmac 5.6 with the ccp4i Refmac5 task?
Can I just copy the 5.6 binary over the 5.5 binary distributed with CCP4?
It looks like the new refmac has a number of new keywords which wouldn't be
accessible doing this, but would it otherwise be compatible? If so, where
does the
Yes. There are two ways:
1) replace $CBIN/refmac5 with refmac5.6
2) on ccp4i click System administration, select configure interface and jus
below
Give full path name for CCP4 programs to overcome name conflicts click Add a
program
There will appear two fields. On the right field type refmac5
Hello,
When I run Refmac with the mixed iso/anisotripic B-value option (refi bref
MIXED), refmac failed with the error message below.
My pdb comes from previous refmac runs with anisotropic B values for all
atoms (H generated but not written).
I just removed from the pdb the ANISOU lines for all
Could you please try refmac 5.6. I think we have fixed this problem. It is
available from:
www.ysbl.york.ac.uk/refmac/latest_refmac.html
You need to take experimental version (it is now fairly stable)
Regards
Garib
On 6 Sep 2010, at 15:01, Lionel Costenaro wrote:
Hello,
When I run
: Monday, September 6, 2010 17:09
Subject: [ccp4bb] Refmac bref MIXED failed
To: CCP4BB@JISCMAIL.AC.UK
Hello,
When I run Refmac with the mixed iso/anisotripic B-value option
(refi bref
MIXED), refmac failed with the error message below.
My pdb comes from previous refmac runs with anisotropic B
Hi Garib,
I tried with refmac 5.6 and the same inputs; it worked fine.
Thanks,
Lionel
2010/9/6 Garib N Murshudov ga...@ysbl.york.ac.uk
Could you please try refmac 5.6. I think we have fixed this problem. It is
available from:
www.ysbl.york.ac.uk/refmac/latest_refmac.html
You need to take
Hi everybody,
I have got a problem concerning refmac5. When try to run refmac following error
occurs:
Free R label has not been set.
I processed my data with xds. Scaling was done by scala. I did this like I
always used to do. So what went wrong?
Thank you in advance,
K
Hi ,
A trivial procedural question.
When running refmac from ccp4i , is there someway that I can have it only
add or substitute columns in the output mtz . I am currently running cad
after refmac to add back in my DAno column and the anomalous intensities ,
but was wondering if there is someway I
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
Hi,
I would like to use Refmac (via ccp4i) to do normal restrained and TLS
refinement. But, I would like all restraints to be removed from one ligand
and one water only (everything else restrained as usual). How can I do
this? I have what I think is a reaction intermediate that I want to be
Dear all,
I have recently installed CCP4 6.1.3 on a MacBookPro running OSX 10.6.2
and cannot get refmac to work.
Can anyone tell me what the Disaster, Disaster! error means.
The exclamation marks seem to imply that it is something very bad:
Truncated output:
CGMAT cycle number =
Katarina Moravcevic wrote:
Dear all,
I am refining a structure of a protein in a complex with phosphorylated
ligand (inositol ring). My problem is that after restrained refinement with
Refmac, the ring is distorted in geometrically impossible ways. Could
anybody advise me on how to deal with
Dear all,
I am refining a structure of a protein in a complex with phosphorylated
ligand (inositol ring). My problem is that after restrained refinement with
Refmac, the ring is distorted in geometrically impossible ways. Could
anybody advise me on how to deal with this problem? Ideally, I
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 ligand OH) and (I think)
refines them as it issues a warning (not INFO), does not say (not be used)
for these and the output .pdb file contains
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
Problem solved.
One must also switch to the make sugar NO keyword. Otherwise Refmac tries
to use the discovered sugar and ion as if it was sugar-peptide bond.
Jan Dohnalek
On Mon, Feb 1, 2010 at 2:52 PM, Jan Dohnalek dohnalek...@gmail.com wrote:
Dear all
I understand that when I use the
Hi,
I just found out, that this effect just occurs when I push the twin
refine button. I have 4 slightly twinned datasets, and so far the twin
refine worked very well...but this should not happen, I think.
Any explanations or advise?
greetings,
Christian
Hi ccp4bb,
I have a big problem
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
Hello again
I am refine my model using TLS and restrained refinement, and I got
below the error message from refmac although the program claim to be
successful. There is no output mtz and pdb files. Any suggestions are
appreciated!
Many thanks!
Jane
***TLS refinement cycle***7
Hello again
I am refine my model using TLS and restrained refinement, and I got
below the error message from refmac although the program claim to be
successful. There is no output mtz and pdb files. Any suggestions are
appreciated!
Many thanks!
Jane
***TLS refinement cycle***7
Hi,
I have a question about the refinement by Refmac program in CCP4 package. I
tried both the old version(1.4.4) and the latest version (2.0.5) for restrained
refinement, and they gave me different result. For old version, it's
0.192/0.250-- 0.191/0.247, while for the latest version,
Hi Feng,
just my speculations (of course, the respective authors of the program
you use may provide you with a better answer):
In terms of refinement results, all pairs of numbers below look the same
to me (regardless the refinement program used):
0.192/0.250
0.191/0.247
0.202/0.254
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
Does anyone know if REFMAC has any SIGFP cutoff? I looked into manual
but perhaps missed it. What I mean is abnormal situation where some
FOBS are 0 or even negative - is there any intrinsic cutoff or
refinement will be done against all the reflections?
Thanks,
Ed.
--
Edwin Pozharski, PhD,
/19/2009 3:55 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] refmac
Hi everyone:
Can someone enlighten me as to the difference between simple scaling
and Babinet scaling in Refmac? It seems to me that Babinet scaling
is more similar to what is employed in CNS for bulk solvent correction
Hi Alexandra,
the answers are in these papers and references mentioned in these papers
(list below is of course incomplete, but following the references inside
of these papers will give you the full picture):
# Jiang, J.-S. Brunger, A. T. (1994). J. Mol. Biol. 243, 100-115.
Protein
The problem is that every directory in lib/data/monomers has to be
world writeable in order to use nfsv4
for refmac to run. Something that clearly I don't want to do...
And why just the monomers directory is refmac trying to write
something, or is it a broken nfslock
I can easily fix
refmac is actually doing when opening the CIF
file.
Is it trying to write something somewhere else?
Thanks
David Jones
Cheers.
--Original Message--
From: David Jones
Sender: CCP4 bulletin board
To: CCP4BB@JISCMAIL.AC.UK
ReplyTo: David Jones
Subject: [ccp4bb] Refmac Problem
I would appreciate if any one has any ideas on this
I have a strange NFS related problem, if anyone has any ideas...
I am running refmac with the ccp4 directories mounted on an nfs
share (v4) mounted under /usr/local
I get the following error...
#CCP4I TERMINATION STATUS 0 Last system
Does it work with NFS v.3?
Cheers.
--Original Message--
From: David Jones
Sender: CCP4 bulletin board
To: CCP4BB@JISCMAIL.AC.UK
ReplyTo: David Jones
Subject: [ccp4bb] Refmac Problem - Permission Denied
Sent: Aug 29, 2009 3:32 PM
I would appreciate if any one has any ideas on this
I
Dear all,
I am refining a structure in Refmac at 2.2 A in win OS. However,
Refmac failed and send this message: forrtl: error (72): floating
overflow
Thank you in advance for your any helpful suggestions.
Best,
Elad
Elad Binshtein
Ph.D student
Department of Life Science
Ben
: [ccp4bb] refmac failed message
Dear all,
I am refining a structure in Refmac at 2.2 A in win OS. However, Refmac failed
and send this message:forrtl: error (72): floating overflow
Thank you in advance for your any helpful suggestions.
Best,
Elad
Elad Binshtein
Ph.D student
Dear
Dear all,
I assume that the current versions (from 5.5.0072) take the input line
twin operator parameters.
However we are getting the Problem get_symm_from_text message whatever
we do.
What is the correct format here?
We do for example
twin operator h,-k,-l
thanks
Jan
--
Dear All,
In absence to an authoritative answer, I'd like to repost my
question. I guess that the overwhelming majority of routine users
will use this auto-weight, and it be nice to know what happens
there.
1) is there an authoritative description somewhere on the site
what refmac precisely
Howdy,
One of our users was trying to re-run some Refmac jobs originally run
with version 5.5.0088 under version 5.5.0092, and he noticed that although
the logfile shows Refmac completing successfully, the new version is not
actually writing the pdb/mtz output files.
He is using linux with CCP4
Dear All,
I am experimenting with manual vs auto-weights in refmac, meditating
about the (cor)relation between -(free)LL, wa, and the B-factor restraint
weights. Questions arising:
1) is there an authoritative description somewhere on the site
what refmac precisely does in auto-weight mode?
Hi,
Sorry to sound stupid, could someone explain what does refmac do if one
chooses mixed (bref MIXED) or overall (bref OVER) B factor refinement in
the context of TLS refinement?
Is it something like: Isotropic for the main chain and/or waters and
anisotropic for the side chain?
Regards,
Hi Partha,
It should be depended on the input model :
MIXEd
Some atoms with isotropic, some with anisotropic B-values. In this
case input file (PDB) defines which atom should be refined
isotropicly and which anisotropicly. The atoms with ANISOU card are
refined anisotropicly.
ta
James Murphy wrote:
I need to model in tetrachloroaurate molecules into a structure, from
our heavy atom soak of Potassium tetrachloroaurate.
I created a pdb file by using chemdraw and exporting as an *.sdf and
opening in pymol and saving as a *.pdb (attached)
The method you used to
I need to model in tetrachloroaurate molecules into a structure, from our
heavy atom soak of Potassium tetrachloroaurate.
I created a pdb file by using chemdraw and exporting as an *.sdf and opening
in pymol and saving as a *.pdb (attached)
I let refmac create a library file (also
It is a bit hard to understand why without looking at the structure..
One reason things get disordered is if the occupancies get misset so
they add up to a number 1.0. In that case REFMAC decided this a a
clash situation and tries to remedy it ..
Could that have happened?
I build alternate
Dear all,
Can any one comment on setting up restraints for refinement against
merohedrally twinned data in Refmac?
I find that refinement distorts the geometry (90% allowed in the Ram.
plot becomes 60% after 10 cycles). Decreasing the weight term to 0.5
or 0.1 seems not to improve the
Dear sir:
I got a very large model with 56 NCS groups working on. So I decided to upgrade
our old version of CCP4, which is 4.6.0. The one I installed is the CCP4 4.6.1
executable for Linux without coot and Databases for Balbes. The installation
appeared to be successful. I can start ccp4 GUI
Dear ccp4bb,
I have noticed I get strange results when I have been attempting to
refine a protein-DNA complex in refmac 5.5.0088. I see a large variation
in the B-factors of connected atoms for the DNA while the protein atoms
all seem to refine to sensible values, for example,
before refinement
Dear CCP4 community,
I would like to refine a structure with two bound ligands using Refmac.
However, the Rafmac GUI allows only one library to be read in. How can I
combine or synthesise two .cif/.lib files (originating from the Dundee DRG
server) and circumvent this problem?
Many thanks in
Alex,
The CCP4i 6.1.1 refmac allows you to combine multiple .cif using Merge
LIBINs. Have you tried that?
Joe
aber...@mrc-lmb.cam.ac.uk wrote:
Dear CCP4 community,
I would like to refine a structure with two bound ligands using Refmac.
However, the Rafmac GUI allows only one library to be
merge monomer libraries under refinement does the trick (amongst others
like combing the textfiles of the cif files)
Thanks,
Alex
Dear ccp4bb,
I've finally gotten around to updating my ccp4 to version 6.1.1 with
the default refmac 5.5.0072 that comes with this from the ccp4
downloads site. I am working on relatively high resolution structures
with a number of alternate conformers for certain amino acids which I
put
Thanks to Robbie Joosten who suggested updating to refmac 5.5.0090
which seems to be happy with alternate conformation again.
I thought it was probably worth mentioning on the list that the ccp4
bundled refmac has this bug.
Simon
On 17 Apr 2009, at 14:07, Simon Kolstoe wrote:
Dear
As far as I know the compatibility has been broken because
of adding new features such as intensity based refinement
or multiple anomalous scatterers to the GUI
Pavol
--
Sent from: Leiden ZH Netherlands.
This is VERY VERY VERY irritating!
Why has it been allowed...
Is there any
This is VERY VERY VERY irritating!
Why has it been allowed...
Is there any advantages??
Eleanor#
Of
JOE CRYSTAL
Sent: 20 March 2009 17:33
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Refmac failed at the end of run
Hi all,
I am using refmac in ccp4i 6.1.1 (installed in windows). It runs well
when using automatic weight, but failed when using user-specified weight
(0.12 in this case). I
Hi all,
I am using refmac in ccp4i 6.1.1 (installed in windows). It runs well when
using automatic weight, but failed when using user-specified weight (0.12 in
this case). I attach the error message as follow. Your help is very much
appreciated.
..
18 0.2064 0.2348 0.846
I'm trying to run 2 refmac jobs at the same time (6.1.0, with updated
refmac 5.5.0070)
When I try to submit the second job I get the message
There is already a job running which will create a file called
tcN1_r15_iso_refmac1.cif
You MUST give an alternative file name
but I haven't
Hi Jon,
I do not think the lib you got from ligand dep is enough to be used in
the refmac.
Unfortunately I can not find or make the library from PRODRG2 server
because the FE can not be handled by that server right now.
So maybe you should make the library yourself : either using sketcher
The right library should be
HEO_mon_lib.cif
Good luck!
leo
Jonathan Marvin Caruthers wrote:
All:
I'm trying to run Refmac with a heme not present in the default libraries.
Unfortunately, I can't get the library sketcher to create a library description
file and get the following error
: 19 December 2008 22:46
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refmac 5.5.063 vs. 5.5.066
The latest version with all the bugfixes will of course appear in
CCP4-6.1.1. Until then, the latest binaries and source codes are
available on the mentioned webpage.
Pavol
I also see such peaks. I have assumed it is because the default in
REFMAC is to use the CuKa SE formfactor, which should be modified at
shorter wave lengths.
(Solution - copy $C:IBD/atomsf.lib and modify Se c to c(CuKa) - f' for
your wavelength.. then assign ATOMSF myversion/atomsf.lib in the
Hi,
Have you specified the right form factor for Se given
the wavelength used in your experiment?
anomalous formfactor [Name] [f'] [f'']
You can also try the new option where you can do simultaneous
SAD phasing and refinement. See: http://tinyurl.com/8on2cr
You will have to upgrade from your
Hi Jan,
the difference between 5.5.0063 and 5.5.0066 is just a few
bugfixes. However, unfortunately one of them introduced a
new bug to 5.5.0066 which has been fixed in the later
versions. Could you please upgrade to the latest version
(currently 5.5.0070) from
Thanks a lot, Pavol,
that indeed did the trick.
refmacRwork Rfree RMSDb RMSDan
5.5.0063 0.1682 0.2118 0.0204 1.717
5.5.0066 0.1781 0.2247 0.0205 1.764
5.5.0070 0.1663 0.2102 0.0204 1.719
Cheers
Jan
On Dec 19, 2008, at 2:21 AM, Pavol Skubak wrote:
Hi Jan,
the
The latest version with all the bugfixes will of course appear in
CCP4-6.1.1. Until then, the latest binaries and source codes are
available on the mentioned webpage.
Pavol
Hello,
I am at a loss on what's going on:
I am refining SeMET containing structure and using REFMAC 5.2.0005 on Linux
and, the same thing happening, using REFMAC 5.5.0070 on Windows.
When MET were modelled, there were no difference peaks anywhere. When I
changed them all to MSE, the large
Dear Michael,
ARP/wARP should recognise this refmac version with no problem. Before
typing './install.sh' just do 'refmac5 -i' to check that refmac is
executed fine and CCP4 environment is setup.
If the problem remains please get back to us with details on the
ARP/wARP version number and
Hello,
Thank you for the reply about the refmac 5.5.0066 error. I downloaded refmac
5.5.0068 but there appears to be a problem for ARPwARP to recognise the
version. I reinstalled ARPwARP and the install shell script freezes when it
looks for the refmac file.
Hi Michael,
thanks for your report. It turned out that 5.5.0066 has a bug
causing crashes. Could you please try the latest version
(5.5.0068) and let us know in case the problem would not
disappear.
Pavol
Hi,
I'm attempting to use refmac to re-calculate a map from a published
structure. Most of the time, this works with no problems.
Occasionally, refmac stops with New ligand has been encountered.
Stopping now.
From the manual, I'd though that using MAKE NEWLIGAND NOEXIT should
prevent this, but
On Saturday 04 October 2008 18:32:00 Engin Ozkan wrote:
Hi everyone,
I was in the middle of creating a Table 1 for a finished structure and
was puzzled by one number. It is the average B factor, especially in
the case of TLS-refined structures. In this case, the average reported
by
Hi everyone,
I was in the middle of creating a Table 1 for a finished structure and
was puzzled by one number. It is the average B factor, especially in
the case of TLS-refined structures. In this case, the average reported
by refmac in the header is the average of the B factors in the pdb
Hi Engin,
you are correct, you have to run TLSANL and report the corrected B-
factor in your table 1.
Jürgen
On 4 Oct 2008, at 18:32, Engin Ozkan wrote:
Hi everyone,
I was in the middle of creating a Table 1 for a finished structure
and was puzzled by one number. It is the average B
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