Le 11/09/2011 00:23, Ed Pozharski a écrit :
> On Sat, 2011-09-10 at 08:21 +0200, Miguel Ortiz Lombardía wrote:
>> A, C and G are RNA nucleotides. T is (mostly) not, its RNA-equivalent
>> is
>> uridine phosphate, U.
>>
>>
>
> Right, that was my suspicion. But I thought that RNA bases would be Xr,
Has anyone had problems with Refmac 5.6? I tried refining our stucture at 1.24
A,
aniso with H in riding position and it just exploded! I get error in distances
such as
Standard External All
Bonds: 3270 0 3270
Angles
I am absolutely sure this has been discussed before, and I have just
re-convinced myself that refmac reports the number of reflections in
just the working set, and not the total number of reflections. So my
question is
Is there a reason why the PDB ADIT tool imports the Nwork from the
refmac pdb
Dear Developers,
it seems to me that at least Refmac 5.6.0117 does not report the actual
lowest resolution used in refinement, but instead the lowest resolution of
the hkl index range generated by the default cif import script instead.
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION
Hi Paul -
Refmac does indeed add riding hydrogens by default; see here:
http://www.ccp4.ac.uk/dist/html/refmac5/keywords/restraints.html#makecif
The REMARK 3 is referring to what you think it is: riding hydrogens have
been added. (They are not, however, written to the output file unless
you
On the interface under Refinement Parameters there are three options
1) Use if present
2) Do not use
3) Generate all
if you are using script then default is generate all (add them riding
positions). You can switch to other options:
make hydr all# generate all - default option
make hydr yes #
Hi,
On Mon, Mar 5, 2012 at 11:52 AM, Matthew Franklin wrote:
> Adding the riding hydrogens generally gives you some improvement in R
> factors even with a good quality (i.e. stereochemically correct) model.
>
and here are the results of more or less systematic test that prove this:
see "On cont
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Pavel,
you may want to add to the structures mentioned in [1] one or two
organic structures present in the Cambridge Database.
"Until recently it was customary to ignore hydrogen atoms throughout the
process of crystallographic X-‐ray structure
Dear Tim,
good catch, thanks; I could craft that phrase more carefully! Although
often it may not be quite fair to take phrases out of context: this
newsletter article was written in the context of macromolecular refinement.
And yes, "recently" may be a broad term -:)
All the best,
Pavel
On Mon,
).
Cheers,
Robbie
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel
Afonine
Sent: Monday, March 05, 2012 21:53
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] REFMAC Riding Hydrogens
Dear Tim,
good catch, thanks; I could craft that phrase more carefully! Although
> Pavel’s statement is likely a bit of an exaggeration, but he has a valid
> (yet hard to prove point). The default in CCP4i was (and is?) to use
> hydrogens only if present in the input file. This is IMO not a safe default.
I agree: what I find confusing here is that the current CCP4i default
is
i GUI?
Thanks again,
--Paul
From: Robbie Joosten
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, March 6, 2012 4:26 AM
Subject: Re: [ccp4bb] REFMAC Riding Hydrogens
Hi Everyone,
Pavel’s statement is likely a bit of an exaggeration, but he has a valid (yet
hard
n
> riding hydrogens a) became available, b) became default, or c) became default
> in the CCP4i GUI?
>
> Thanks again,
>
> --Paul
>
>
>
>
> From: Robbie Joosten
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Tuesday, March 6, 2012
Thanks again,
>
> --Paul
>
> From: Robbie Joosten
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Tuesday, March 6, 2012 4:26 AM
> Subject: Re: [ccp4bb] REFMAC Riding Hydrogens
>
> Hi Everyone,
>
> Pavel’s statement is likely a bit of an exaggeration, but he has a vali
re present?
> >
> >
> > Also, how about refmac version numbers? Is there a clear
> > demarcation when riding hydrogens a) became available, b) became
> > default, or c) became default in the CCP4i GUI?
> >
> >
> > Thanks again,
> >
> >
> >
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 w
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 refma
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 wrote:
> Hi,
>
> I am using REFMAC 5.2.0019 to run the following script:
> ***
> refmac5 hklin a xyzin b < REFI
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 wrote:
> Hi,
>
> I am using REFMAC 5.2.0019 to run th
: ianj...@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 i
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.
Haili
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 a
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, 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 more second qu
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 tha
Dear All:
I use Refmac5 to refine my structure model.
When I set the sigma value to 0.3 (as recommended from tutorial), the
resulted model has many red-bars by coot validation (geometry, rotamer,
especially, Temp Facotr).
I then lower the sigma value to 0.1, the resulted model is much improved b
hello everyone
Does anybody knows why refmac5 will not process any model that
contains thymine in its structure? This problem only happens on my PC
which supports a 2.1.0 version of ccp4i. The error in the log file
says its due to bad value during floating point read. However, this
proble
Yes, it's called a "partial structure". You input the mask as
structure factors and call them "FPART" in the refmac LABIN input.
http://www.ysbl.york.ac.uk/refmac/docs/keywords/xray-principal.html#labin_fparti_phiparti
Then enable refining the scale and B factor of the partial structure:
http://w
Thank you very much James !
-kiran
From: James Holton
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, September 26, 2012 9:58 PM
Subject: Re: [ccp4bb] Refmac- solvent mask
Yes, it's called a "partial structure". You input the mask as
structure f
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
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
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
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
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
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
Sorry - Garib points out form factors are there - labelled atom type
scat cromer ...
You shoulfd find SE if there is a SE atom in the pdb file
Eleanor
loop_
_atom_type_symbol
_atom_type_scat_Cromer_Mann_a1
_atom_type_scat_Cromer_Mann_b1
_atom_type_scat_Cromer_Mann_a2
_atom_
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 mes
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
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 advant
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 ccp4
On 24/08/17 16:29, Dr A.A. Jalan wrote:
I am trying to change the default refmac run parameters in coot. For
this, I created a refmac-extra-params file in the directory from where
coot is launched.
(set! refmac-extra-params (list "MAKE HYDROGENS ALL" "REFI BREF ANIS"))
You can set refmac-
Dear Prof Emsley
That worked!
Thanks
Abhishek
On 2017-08-24 17:42, Paul Emsley wrote:
> On 24/08/17 16:29, Dr A.A. Jalan wrote:
>
>> I am trying to change the default refmac run parameters in coot. For this, I
>> created a refmac-extra-params file in the directory from where coot is
Dear all,
How does one exclude water from anisotropic refinement in refmac5.8 under
ccp4-7.0
Here is the relevant section from the com file,
refi -
type REST -
resi MLKF -
meth CGMAT -
bref MIXED anisou residues from 100 A to 200 A
This does not work and the logfile has the foll
Dear all,
I am refining structures containing disulfides using refmac. Many of the
disulfides are partly broken due to radiation damage.
I tried modeling alternative conformations (i.e. one cysteine pair in a
disulfide and the other pair as free thiols), but after refinement the reduced
form i
Dear Refmac developers,
I am trying to reproduce some successful refmac runs but cannot get the
previous results despite playing around with the parameters.
I did those runs in Feb 2014 (Refmac 5.8.0049) but unfortunately have
overwritten the log files in a backup. I still have the pdbs, mtz
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
l
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
--
=
bject: [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 st
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 er
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, Ass
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 would
The numbers do make sense now: AaA, AbA, etc, correspond to different HETATM
groups and (what was confusing me a lot) the No. atoms includes riding
hydrogens.
On Thursday, 2 May 2019, 23:27:49 BST, Jonathan Cooper
wrote:
In the output statistics part of the GUI there is table of mean
Just double checking that Refmac automatically handles twinning without
the need for a keyword or a box click in i2. I have a crystal in P32 21
that gives poor Rfactors and maps (Rfree mid 40s) from what should be an
excellent model. I have reprocessed in P32, P1 and C2 but all give
similar re
Yes - I am having problems with hydrogens in REFMAC recently - has
something changed?
My problem is this: Build a rough model for some residues into a lousy map.
(R ~ 32% etc..)
I know it is rough with clashes and bad geometry but trust refinement to
improve things a bit..
However if the run includ
The first thing you want to do when debugging hydrogens in refmac5 is to
make sure it outputs whatever it was doing:
MAKE HOUT Y
This is not the default. Normally, refmac will take a PDB file without
any hydrogens in it, quietly add them before doing refinement, and then
delete them before ou
Hi Dale,
Yes Refmac uses the dictionaries found in lib/data/monomers
Of course these targets may differ from those used by validation tools.
If you identify anything that's clearly wrong then do let us know!
Regards,
Rob
> On 25 Jul 2020, at 17:22, Dale Tronrud wrote:
>
> Hi,
>
> I'm seeki
Hello, I'm not totally up-to-the minute with this but I didn't know that refmac
itself added waters so maybe it's another program in an i2 pipeline, or
something. However, I know another excellent refinement program that does ;-)
and an excellent graphics program that does, too ;-0
In the past,
Dear Jon,
thanks for your answer. Maybe I have been too quick in writing my last message.
The point is that with the old CCP4 interface, I would have been able to run
Coot-findwaters to automatically add and remove water molecules at certain
DELFWT and FWT rmsd tresholds, respectively, through
You don’t say quite how you are doing this. There is an option in the i2
pipeline to add waters using coot when the r factor falls below some
assigned value.
This is done using COOT.
One can debate whether it is a useful option or whether the user would be
better o open COOT and supervise the water
Hi Luca,
as Eleanor mentioned, in the i2 interface there is in the option menu an
add water button. That will automatically run the coot find waters script
similar to the old interface. Paul did use some very sensible values to
look for blobs, which might be waters. These ones are used (basically
nal Message-
> From: CCP4 bulletin board On Behalf Of Ian
> Tickle
> Sent: Wednesday, December 2, 2020 15:02
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Refmac not handling microheterogeneity?
>
>
> Dear All
>
> I just downloaded a PDB file (7A5V) from the EBI se
t; said, 1 in 6 missing PDB-REDO entries is caused by this problem, so a
> solution would be very welcome.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board On Behalf Of Ian
> > Tickle
> > Sent: Wednesday, December 2, 2020 15
s no clean solution for this and I imagine this problem goes
>> very deep into the internal representation of the model in REFMAC. That
>> said, 1 in 6 missing PDB-REDO entries is caused by this problem, so a
>> solution would be very welcome.
>>
>> Cheers,
>> Robbi
SCMAIL.AC.UK>> On Behalf Of Ian
> Tickle
> Sent: Wednesday, December 2, 2020 15:02
> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> Subject: [ccp4bb] Refmac not handling microheterogeneity?
>
>
>
.50 59.05 N
> >
> >
> >
> >
> > In case 1 OD1 A is immediately followed bu OD1B
> >
> >
> > In second case - all As listed then all Bs
> >
> >
> > Eleanor
> >
> >
> >
> >
> >
uftrag von
Santarsiero, Bernard D.
Gesendet: Mittwoch, 17. September 2014 14:20
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] REFMAC - TWIN OPTION
Can someone point me to bulletpoint documentation on using the twin refinement
in CCP4?
Here's what I did.
1. I'm in space group P3, and
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 in
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 refm
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, K
Simon,
REFI BREF OVERALL should do something close to what you're looking for (it
will refine a single B-factor for the entire model, but there shouldn't be
variation within the model).
Not sure where (or if) this is in the gui, however.
Pete
>
> Dear all,
>
> I have a structure at fairly low r
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
MAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and B factors
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
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
> 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
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 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
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
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
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
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 all -
I seem to be encountering a problem with Refmac refinement of a
structure containing anisotropic B factors. I have been using TLS
refinement and individual anisotropic B refinement, which may not be
correct technique, but it does lower my R and Rfree versus aniso B
refinement alone
I'm running into some geometry problems with my DNA model after refinement with
refmac (version 5.5.0109), and would appreciate any feedback.
The problem is that the angles for many of the glycosidic bonds are 2 to 4
degrees off of the ideal values, and so are several standard deviations outsid
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Dear Kenneth A. Satyshur,
what is your weight set to? If it is set to 'auto', try setting it to a
specific value and lower that value until the explosion stops.
If this happens at low matrix values (at 1.24A it should be way above 5
or 10 for a well
x27;t work, we may need a closer
look at your input model.
Cheers,
Robbie
> Date: Thu, 27 Oct 2011 20:48:49 -0500
> From: satys...@wisc.edu
> Subject: [ccp4bb] refmac 5.6 ccp4 6.2.0
> To: CCP4BB@JISCMAIL.AC.UK
>
> Has anyone had problems with Refmac 5.6? I tried refining ou
Just to verify, is this by any chance *unrestrained* refinement?
On Fri, 2011-10-28 at 09:37 +0200, Tim Gruene wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Kenneth A. Satyshur,
>
> what is your weight set to? If it is set to 'auto', try setting it to a
> specific value and l
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Hash: SHA1
Dear all,
If those hydrogens are in riding position, their coordinates are
calculated and should not be refined at all, isn't it? Hence they should
appear in the list of deviations at all.
Are the hydrogens present in the PDB file? Does it work to de
Hi All,
Is it possible to define twin operator and twin fraction in the latest version
of Refmac (i.e., in version 5.6.0117) ?
I tried to define these two keywords in Buccaneer but it fails with an error
message "Refmac_5.6.0117: Problem in some of the instructions".
Please help me to fix this.
Hi Bernhard
So what's new? See
http://ccp4bb.blogspot.com/2011/11/pdb-header-info-wrong.html
(17-Nov-11).
Cheers
-- Ian
On 2 January 2012 06:58, Bernhard Rupp (Hofkristallrat a.D.)
wrote:
> Dear Developers,
>
> it seems to me that at least Refmac 5.6.0117 does not report the actual
> lowest
> So what's new?
Alzheimer's and late night senile dementia :-)
BR
PS: nice site!
-Original Message-
From: Ian Tickle [mailto:ianj...@gmail.com]
Sent: Monday, January 02, 2012 4:34 AM
To: b...@hofkristallamt.org
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] refmac l
Dear All,
When running refmac with twin refinement option it continues
indefinitely at "trying gamma equal" step. With normal refinement
this problem is not there.
Any idea, how to rectify this?
Jobi
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 Ref
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
Hi Garib,
I tried with refmac 5.6 and the same inputs; it worked fine.
Thanks,
Lionel
2010/9/6 Garib N Murshudov
> 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 ve
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 i
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 hav
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
Hi, Alex:
> Which sigma do you mean?
The one for automatic weight, not for Jelly-body refinement.
I did not turn the "Jelly-body refinement" on.
Thanks
Ros
On Thu, Apr 26, 2012 at 4:08 PM, aaleshin wrote:
> Hi Uma,
> Which sigma do you mean? The one for Jelly-body refinement?
> J-B sigma=0.
Hi Uma,
Altering sigma affects the strength of geometry restraints throughout the model
- bonds, angles, etc. Choosing a very low sigma will cause geometry to be more
tightly restrained towards "ideal" values, which is why you observe
improvements in Coot validation. Note that strengthening th
metric
restraints too much.
Best regards,
Herman
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Robert Nicholls
Sent: Friday, April 27, 2012 9:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refm
-factor model).
Note that the absence of geometric outliers does not prove that your model is
optimal. If you use too tight restraints you can end up hiding genuine fitting
errors.
Cheers,
Robbie
Date: Fri, 27 Apr 2012 10:04:11 +0200
From: herman.schreu...@sanofi.com
Subject: Re: [ccp4b
).
> Note that the absence of geometric outliers does not prove that your model
> is optimal. If you use too tight restraints you can end up hiding genuine
> fitting errors.
>
> Cheers,
> Robbie
>
> --
> Date: Fri, 27 Apr 2012 10:04:11 +0200
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