Hi, I'm having a bit of ccp4i input- vs refmac logfile disconnect:
For my NCS definitions in refmac (5.5.0036), via ccp4i (v6.0.2):
Input
* I select Tight main chain and medium side chain from the dropdown.
* I reset the NCS Bfactor weights to 10 for both tight, and medium
ncs
Thanks to both, in the end I downloaded the new version of refmac and moved the
characters,
Louise
- Messaggio Originale -
Da: Eleanor Dodson [EMAIL PROTECTED]
Data: Martedi', Agosto 19, 2008 6:00 pm
Oggetto: Re: [ccp4bb] Refmac problems on Mac OS X Leopard
A: Louise Gourlay [EMAIL
Dear All,
I installed CCP4 on my Mac OS X Leopard system using fink. I have some problems
with Refmac, it doesn't refine calcium or chlorine atoms, or any non-protein
atom in general. In the log file it doesn't recognize them and says:
FORMATTED OLD file opened on unit 45
Logical
: [ccp4bb] Refmac problems on Mac OS X Leopard
A: CCP4BB@JISCMAIL.AC.UK
Dear All,
I installed CCP4 on my Mac OS X Leopard system using fink. I
have some problems with Refmac, it doesn't refine calcium or
chlorine atoms, or any non-protein atom in general. In the log
file it doesn't
I got round this problem by downloading the most recent version of
Refmac from Garib Murshudov's website.
Alice
Alice Dawson
Division of Biological Chemistry and Drug Discovery
University of Dundee
Dow Street, Dundee, UK
[EMAIL PROTECTED]
to the structure with coot.
Also, I forgot to say that the refinement works when I use another computer so
it's something to do with mine.
Thanks,
Louise
- Messaggio Originale -
Da: Louise Gourlay [EMAIL PROTECTED]
Data: Martedi', Agosto 19, 2008 4:26 pm
Oggetto: [ccp4bb] Refmac problems on Mac OS
Hi all,
kind of a weird problem - the R-factors of a refinement using the new
twin refinement in refmac are low, almost suspiciously low:
A good 1.9AA data set, space group H3/R3, many statistics starting
with truncate's cumulative intensity distribution clearly suggest
twinning. The
Jan Abendroth a écrit :
Hi all,
kind of a weird problem - the R-factors of a refinement using the new
twin refinement in refmac are low, almost suspiciously low:
A good 1.9AA data set, space group H3/R3, many statistics starting
with truncate's cumulative intensity distribution clearly suggest
Hi Wim,
Am 14.08.2008 um 13:53 schrieb Wim Burmeister:
...
Twinning has two effects:
The effective ration of observations/variables decreases with
increasing twinning fraction.
...
I don't know how REFMAC5 handles twinning, but if the structure is
simply split into two identical parts,
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
Dear Mitch,
I did not run uniqueify but i have added free-R flags by running xdsconv with
extra command line in in-put file
GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05
Dear Leo,
This 94.5% is total completeness of the data.
I am pasting below the header information in that PDB file.
REMARK 3
Akhter
Sent: Friday, August 08, 2008 2:20 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac out-put file header information
Dear Mitch,
I did not run uniqueify but i have added free-R flags by running xdsconv with
extra command line in in-put file
GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05
:[EMAIL PROTECTED] On Behalf Of Yusuf
Akhter
Sent: Friday, August 08, 2008 2:20 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac out-put file header information
Dear Mitch,
I did not run uniqueify but i have added free-R flags by running xdsconv
with
extra command line in in-put file
Thank you very much to Artem, Lijun, Dale and Paul for giving me great
suggestions regarding my earlier query on D to L amino acid residues.
Now one more problem is in same 3 A structure refinement. For those who not
remembered my case. I have processed a diffraction data-set at 3 A using XDS. I
Dear Yusuf --
On 8 Aug 2008, at 06:01, Yusuf Akhter wrote:
My data is 95.4% of completeness at Signal/noise
=-3.
I noticed that in the header of out-put PDB file from Refmac shows
100%
completeness.
Could you precise where do you see 100% completeness in the PDB
header (overall
Hi, my refinement (Refmac_5.2.0019) in sp. grp. C2 with 2 TLS groups,
bulk solvent, and overall anisotropic scaling gives the following
output:
-
Overall : scale =1.143, B = 0.148
Babinets bulk
Dear All,
I have looked everywhere for answers on this one with no luck... I
have several structures at reasonable resolution 1.7 to 1.1A. I have
performed unrestrained refinement on the model which is fine for the
core protein and ligands but the surface atoms start flying off a bit.
Hi Matthew
It would be easy to edit the ligand restraint dictionary make all the
sigmas very big (assuming the input CIF routines don't perform sanity
checks on the values!): that would make it unrestrained to all intents
purposes. But when you say that unrestrained refinement is 'fine' what
It would be possible with a bit of effort to apply such mixed restraints
using SHELXL. However I'm not convinced that it is such a good idea, at
the resolutions you are working at the geometry of the core regions will
be primarily determined by the X-ray data anyway. Perhaps what we
really need
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of George M. Sheldrick
Sent: 04 July 2008 13:42
To: Matthew BOWLER
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac unrestrained refinement on ligands only
Perhaps what we
really need are B
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 Refmac web page today. Is that file
mirrored somewhere, or can someone provide it to me? Thanks. Tom
--
Thomas J.
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
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:
Dear All,
I occasionally get the following error after running refmac:
#CCP4I TERMINATION STATUS 0 Error from script
/home/local/LINUX/ccp4-6.0.2/ccp4i/scripts/refmac5.script: error writing
stdout: I/O error
The above error is from the last lines of the log file. It seems that
refinement
Kianoush wrote:
Dear All,
I occasionally get the following error after running refmac:
#CCP4I TERMINATION STATUS 0 Error from script
/home/local/LINUX/ccp4-6.0.2/ccp4i/scripts/refmac5.script: error
writing stdout: I/O error
The above error is from the last lines of the log file. It seems
I agree with Paul and George that it is vital that PDB files from TLS
refinement contain ANISOUs which reflect the results of that refinement,
and would like to reinforce Paul's point below.
There are many possible parameter-frugal approximations to full
ADP-refinement: TLS is just one of
We do have to mess with the PDB format every time something new is
invented. Usually it's just REMARK 3 that has to be changed, but you
always need to put some kind of remark in the header that you used a
certain type of refinement.
When different types of anisotropic refinement are combined
My experience is the same as Frank's. As I compete a structure for which
I am using TLS restraints, I often refine in both phenix and refmac and
sometimes go back and forth. I am confused as to why refmac keeps the
ANSIOU cards and doesn't keep its output consistent. It would be nice if
Hi, here's what triggered my earlier rant:
I took a pdb from phenix.refine back into refmac, with same TLS
definitions, but leaving the ANISOU cards in (accident). I ran this
through TLSANL, asking for total B.
Refmac has left the ANISOU cards, but all zero except the first
element. ATOM
Some comments:
- We (the PHENIX developers) are working with the PDB to come up with
a more
streamlined deposition of TLS information for PHENIX. There are
some other
issues that need to be resolved first that have slowed this down a
little.
- I am in agreement with George (not
Hi All,
I'm refining a structure of a protein DMA complex at 1.8A resolution.
The spacegroup is P21 and the DNA is pseudopalindromic. It looks like
I have electron density for mixed base pairs outside the palindromic
region, but Refmac5 complains when I try to model it.
ERROR: in chain E
I keep finding that the Refmac version from 5.4.0034 is more stable
at least with full anisotropic refinement at 1.35 Å resolution. The R-
factor stays relatively similar and there is a slow decrease of R-
free with R-work. It doesn't jump around compared with an identical
refinement in
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
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
Thanks for those pointing out my cut and paste error. Below are the
correct numbers. The first term of the formfactor is almost twice as
high compared to the other version. I suspect it is because the
newer version is using the wavelength in the calculation, and the old
version didn't.
Garib,
Many thanks for pointing out the differences. A couple of more
questions:
1. Could you tell me how 5.4.0033 by default handled the free and
missing reflections in map calculation. Also, is the ccp4i interface
suitable for the latest version of refmac --- I add the extra
Hi
I usually add extra keywords in the developers option section of
the interface. I hope we will soon change the interface ti suite
current and the next version
of the program.
If unobserved reflections are present in the mtz file with missing
reflection flag then for map coefficients
Hi,
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 atom have
changed dramatically even though I'm using the same anom formfactor
SE -8.13 5.05
Hi all,
I hope everyone is having a nice holiday break. I want to refine the
B's anisotropically of only the selenium atoms. Does BREF MIXED
option work in REFMAC? Do I need to pre-calculate the ANISOU
parameters or can I just enter a blank ANISOU card?
Thanks,
Mark
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,
I'm wondering what's the best way to add an extra (tighter) distance
restraint on the linkage
between the P-atom of a guanidine (Gd)-residue and the O3'-atom of a
thymidine (Td)-residue in an oligonucleotide structure,
with use of the program Refmac_5.2.0019 (ccp4-6.0.2)...?
And
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
Dear Jason,
you will have to include the planarity either by introducing torsion
restraints for the specified bonds, or by using the plane definition.
Pls. be aware that in the current refmac versions the plane definitions
will be used with a fixed sigma, i.e. the value of the dictionary is not
Dear all,
How does one tell Refmac that the bond between two non-amino-acid
monomers should be planar (in the case that this bond is an amide)?
My ligand has amino-acid and non-animo-acid constituents that are
connected via amides. I have made library definitions for all of the
non-standard
You havent got an incorrect CISPEP definition lurking in the PDB file
have you - COOT does NOT correct these so if you rebuild something which
has been previously flagges as CISPEP ( and that can happen if a very
ugly omega angle falls to 89.999 ) then it stays that way in the PDB
output from
You need the atom name CA and CL moved one space to the left relative to
C O N etc..
And correct the atom type in cols 76?? from C to CL and CA ( again moved
one space to left)
Eleanor
Vineet Gaur wrote:
Hi all
i am having Ca2+ and Cl- as hetroatoms in my protein structure. while doing
Hi all
i am having Ca2+ and Cl- as hetroatoms in my protein structure. while doing
refinement with REFMAC i m getting following warnings:
I am reading library. Please wait.
mon_lib.cif
WARNING : residue: CA994 chain:XX
different element name: file:C
Dear Vineet,
It seems, in your input PDB file the atom level for CA and CL in the last
column is C. It should be CA CL respectively. The atom name in the
input file and Dictionary doesn't match.
all the best
Manish
Vineet Gaur [EMAIL PROTECTED] wrote: Hi all
i am having Ca2+ and Cl-
Hi -
A quick note -
We (with Chris Ulens) have seen recently in one case that in a case
MATRIX AUTO would give 'excessive' RMSD, close to 0.030.
Checking the cell based on the projection of RMSDs to the cell axes,
a utility kindly provided by WHATCHECK,
it was suggested that the cell
.
Karolinska Institute
Stockholm, Sweden
___
- Original Message -
From: Mark Mayer [EMAIL PROTECTED]
Date: Tuesday, September 11, 2007 10:08 pm
Subject: [ccp4bb] refmac auto matrix weight - 'reasonable' rmsds
To: CCP4BB@JISCMAIL.AC.UK
Hello all,
I
Quoting Anastassis Perrakis [EMAIL PROTECTED]:
On Aug 9, 2007, at 15:02, Tommi Kajander wrote:
so, a) WHAT IS GAMMA??
gamma is possibly the letter of the greek alphabet that has had most
abuse from scientists.
thats what i thought...
dear all (well experts i suppose),
can someone explain what this means (REFMAC):
Resolution limits= 19.944 2.600
Number of used reflections = 12652
Percentage observed = 100.
Percentage of free reflections = .
On Aug 9, 2007, at 15:02, Tommi Kajander wrote:
so, a) WHAT IS GAMMA??
gamma is possibly the letter of the greek alphabet that has had most
abuse from scientists.
http://en.wikipedia.org/wiki/Gamma_%28disambiguation%29
seriously now, I have seen that as well, but never increasing to such
Dear CCP4bb
thanks so much for the helpful information regarding carbohydrate
refinement. Kim's recommendation (see below) for the validation server
worked really well and helped me to finally figure out what is going on.
Seems as if REFMAC5 (part of ccp4-6.0.2 version) is not handling
Dear all,
I am trying to refine N-linked carbohydrates with REFMAC5 (CCP4 version
6.0.2) - however - it seems as if I am unable to get the stereochemistry
right (when I tried to deposit the structure to PDB - they complaied about
it). My protein comes from D. melanogaster and I can see density
Two things I think
1) I is a metal so you need to move the atom name 1 space to the left -
more like this:
ATOM 2838 O HOH W 102 6.018 39.720 31.127 1.00
21.43 O
ATOM 2839 I I B 1 19.956 22.770 18.597 1.00
30.00 I
And the monomer library
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
Subject: Re: [ccp4bb] refmac fails on iodine ions
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
Date: Thu, 31 May 2007 14:38:42 +0100
From: Stephen Brian Carr [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Subject: refmac crashes when ncs restraints applied
Message-ID: Pine.VMS.3.91-2 (vms)[EMAIL PROTECTED]
MIME-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
Dear CCP4 users,
I am
Date: Thu, 31 May 2007 14:57:03 +0100
From: Stephen Brian Carr [EMAIL PROTECTED]
To: ccp4bb@jiscmail.ac.uk
Subject: refmac crashes when ncs restraints are applied
Message-ID: Pine.VMS.3.91-2 (vms)[EMAIL PROTECTED]
MIME-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
Dear CCP4 users,
I
I certainly have used NCS restraints with ccp4-6.0.2
That doesnt help much though does it!
Eleanor
[EMAIL PROTECTED] wrote:
Date: Thu, 31 May 2007 14:57:03 +0100
From: Stephen Brian Carr [EMAIL PROTECTED]
To: ccp4bb@jiscmail.ac.uk
Subject: refmac crashes when ncs restraints are applied
It's guessing time, but it looks like you don't have write permission to
the directory in which ccp4i/refmac is trying to direct the output file
(or maybe the directory no longer exists, etc).
Jhon Thomas wrote:
Hi all
I am using CCP4i, and running refmac for the
refinement
Yes, it is available in the GUI...
Flip
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Peter
Adrian Meyer
Sent: Wednesday, May 09, 2007 23:28
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and B factors
Simon,
REFI BREF OVERALL should do
@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and B factors
Thanks very much for the replies, and especially for the link to the
previous thread on this topic (Eva).
Just a comment about the ccp4i GUI in general - pretty much all the students
in my department are slowly becoming dependant on the GUI
2007 10:21
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4 GUI (was:RE: [ccp4bb] Refmac and B factors)
Hi Simon,
Well, X-ray crystallography nowadays often, but certainly not always, amounts
to running a set of programs with default settings with a few mouse clicks in
the GUI. The fun part
bulletin board [mailto:[EMAIL PROTECTED] On
Behalf Of Kolstoe S.E.
Sent: Thursday, May 10, 2007 5:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and B factors
Thanks very much for the replies, and especially for the link
Hi Simon,
you can't stop it - I asked the same question (with some more questions)
some weeks ago.
You can find the original email and the tips I got for not-so-good
resolution B-factor refinement here:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html
Good luck,
Eva
2007/5/9,
All,
We are currently refining a 1.6A structure with Refmac5. There are a
few loops with backbone geometries that Refmac seems to have an issue
with. There is clear density for the modeled conformations, however
when doing restrained refinement the following errors are encountered
and the
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
If a pdb file contains some residues that have multiple conformations,
when using refmac to refine it, will the programm take consider of
these conformations? It seems that refmac would do this but I am not
very sure. I downloaded a structure with some conformations from the
pdb, but after
SHELX does not need a parameter to control the relative weights of
restraints and X-ray data, it is performed automatically. However you
can change the restraint esds, either individually or globally using
DEFS, though the default values are generally OK. There is bound to be
some difference
Dear CCP4BB users;
Due to mixed state of a ligand conformation I wanted to use
shelx, to refine it correctly at the end point of refinement.
My problem is, that I do not know how to control geometry in Shelx.
After Shelx refinement, my bonds are very tight (rms 0.008), angles
loose (rms ~1.9),
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