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 pr
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 di
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
Since version 5.5.0066 is the version in ccp4-6.1.0, is there going
to be a patch?
On Dec 19, 2008, at 12:32 PM, Jan Abendroth wrote:
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
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 difference
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
http://www.ysbl.york.ac.uk/~garib/re
Hi all,
puzzled by an increase of R-factors when switching to the new ccp4 and
along with it from refmac 5.5.0063 to 5.5.066, I took a closer look.
Same refinement, same input (in fact, started from the interface with
re-run job) gives distinctly different statistics. It appears to be
only
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 com
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
Hello,
I have attached a log file from a refmac refinement output that was initiated
by ARPwARP (the flexwarp program in CCP4) after an initial model building was
determined good. This is the refmac model refinement when the ARPwARP program
starts a separate job to refine or finalize the mode
Thanks for the quick reply.
I got the noexit option for the ccp4-6.0.2 html, so you might have
already started adding it.
I've had no luck with 5.2.0019 (ignores either keywords, stops with new
ligand message) and 5.4.0077 (ignores noexit, fatal error for continue).
I'll give it a try with the l
The keyword is
make newligand continue
(I need to add noexit option. It makes sense)
regards
Garib
On 26 Oct 2008, at 22:10, Pete Meyer wrote:
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, refm
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
>
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 f
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, 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 r
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 Gour
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
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]
4:26 pm
Oggetto: [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
Can you send a bit of your PDB including the CA and CL? Eleanor
Louise Gourlay wrote:
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 do
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 nam
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
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, eac
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 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 structu
king the
> box to complete the reflection list and extend your
> input freeR set.
>
> Regards,
> Mitch
>
>
> -Original Message-
> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Yusuf
> Akhter
> Sent: Friday, August 08, 2008 2:20 AM
> To
] 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
GENERATE_FRACTION_OF_T
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
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 reflect
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
a
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
Babinet"s bulk solve
> -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
> Perhap
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 a
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' wha
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.
S
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
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. Magl
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:
How to keep a ligand fixed during refinement using refmac?
Debasish
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 seem
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
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 (sa
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 them
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
the
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 unusual
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 B
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 res
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 cu
Murshudov <[EMAIL PROTECTED]>
Date: Wednesday, January 2, 2008 19:19
Subject: Re: [ccp4bb] Refmac 5.4.0066 versus Refmac 5.4.0034
To: CCP4BB@JISCMAIL.AC.UK
On 2 Jan 2008, at 17:15, Ethan Merritt wrote:
On Tuesday 01 January 2008 06:40, Mark A Saper wrote:
Well, I gue
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:
--- 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: CCP4BB@JISCMAIL.AC.UK
>
> > On 2 Jan 2008, at 17:15, Ethan Merritt wrote:
>
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
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 atom have
> changed dramatically even t
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
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
keywords
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.
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 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
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
__
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 i
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
Hello,
I'm running a TLS refinement with Refmac and keep getting the following output
in my logfile.
B ARRAY FOR HESSIAN TABULATION TOO BIG
VALUE RESET TO MAXIMUM
On the next round of refinment e.g below everything seems normal, but each
cycle end with this
warning. Can I (should I) set the
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 C
Hi all,
along the lines of a recent discussion:
At the final stages of the refinement of a structure which a whole bunch of
ncs (2x4chains) at 2.2A resolution in P1, I run into the following very
annoying and persistent problem. The Ramachandran plot shows a whole bunch
of ugly outliers. While some
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
refin
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 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 "
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 migh
Just to add to the outliers in Refmac - careful when some of your atoms
have zero
occupancy. The bond restraints are not applied any more to these atoms
(my feeling) and
CERTAINLY are NOT CHECKED FOR OUTLIERS by Refmac at the end of the
refinement.
Jan Dohnalek
Eleanor Dodson wrote:
No comme
No comment on the Auto debate, but the RMSD of bonds is a crude measure
unless you check the outliers..
You can make REFMAC list these - I think it should do so by default
actually..
Bad metal distances for instance can distort the number enormously.
Eleanor
Mark Mayer wrote:
Hello all,
I b
t; 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@JISC
mistry & Biophysics Dept.
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'
Hello all,
I believer the suggested matrix weight for running refmac is 'auto'. I'm at the
end of refinment for
a data set that I've cut at 1.59 A, so maps are pretty. Here's the logfile with
auto weighting ...
NOTE bond rmsds !!!
REMARK 3 R VALUE(WORKING SET) : .15481
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...
> http://en.wikipedia.org/wiki/Gamma_%28di
Dear Tommi,
a) WHAT IS GAMMA??
Gamma is a factor used in the Refmac minimization procedure.
In most cases Refmac achieves convergence with gamma = 0.0.
In case the program fails to reach convergence with gamma = 0.0, gamma
is increased stepwise. This generally facilitates convergence.
Regards,
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 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 = .
Overall
Dear CCP4ers,
I have just installed the latest CCP4/CCP4i (6.0.2/1.4.4.2) under OSX
10.4.9. When I run refmac using the gui even though I have not checked
the box "generate weighted difference maps..." the programs tries to
create the maps. Is there an easy way to prevent this. Since I am using
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
alpha-L-fuc
you can use
http://www.glycosciences.de/modeling/sweet2/doc/index.php
to get a pdb file of your sugar
and after fitting in density and refinement use
http://www.dkfz-heidelberg.de/spec/glycosciences.de/tools/pdbcare/
to check the stereochemistry
this should identify if there is a refmac di
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 for
@JISCMAIL.AC.UK
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
> To: CCP4BB@JISCMAIL.AC.UK
> 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] wro
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
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 cal
> Dear All,
>
> I am having trouble with refmac dictionaries when refining a
> structure that contains an iodine ion.
> the PDB entry should be correct and according to the convention
> (water added for comparison):
> -
> ATOM 2838 O HOH W 102 6.018 39
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
Message
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:
MIME-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
Dear CCP4 users,
I am running refmac 5.2.0019 in ccp4 6.0
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:
MIME-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
Dear CCP4 users,
I am running refmac 5.2.0019 in ccp4 6.0.2 on a
Hi Jhon,
It might not be the source of the problem, but this error can occur if
you have closed the terminal window from where you started ccp4i while
still running ccp4i. i.e. if you back-grounded ccp4i when you started
it. Jobs such as Refmac invoke a "Movefile" command which sometimes
writ
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
Hi all
I am using CCP4i, and running refmac for the
refinement of the my data. I have ran this many times earlier
successfully. Now as i run the refamc5 , it runs successfully and
complete the job,but
not writing any output file.
At the end of the logfile, i get a sat
CCP4 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 t
Hoedemaeker
Sent: 10 May 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
t
To: CCP4BB@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
301 - 400 of 414 matches
Mail list logo
