Dear ccp4 members
I have something that surprises me with molecular replacement. I have obtained
a
solution for a single point mutation using Phaser, the solution seems ok. I do
one round of refinement with refmac and I check the structure using molprobity
before I even start really to refine
Hi Careina,
I can think of two possibilities:
- your restraints are not strong enough.
- if your mutant dataset is of significantly lower resolution than the native,
almost any refinement will make the model worse. If this is your case, just
change the mutated residue and very, very obvious
Dear all,
Could any one help me regarding my serious problem actually i have collected
data at 3.0 and cut off 3.1 where
the data statics showed the good values for the further processing.
According to the methew coefficient there would be two molecule in the
asymmetric
unit but after
If possible refine restraining to the native structure (I only did this a long
time ago with TNT with a script Jan Pieter Abrahams wrote, I don't know if
refmac has this possibility).
Prosmart generates restraints for use in refmac:
http://www.ysbl.york.ac.uk/mxstat/Rob/index.html
It worked
Hi,
The R-factor you mention, is it an R-factor before any refinement of the
model ? Like an R-factor at the very beginning of the entire modeling
procedure, right after molecular replacement ?
If this is so: you should always compare such initial R-factors to the
R-factors for the atoms
Rex, I think the problem is that the latest version of the dictionary which
contains LBT (and many other new ligands) only works with Refmac 5.6 (but
check with Garib on that!), but that version hasn't yet been compiled for
Windows. Unfortunately Windows versions tend to lag a bit behind Linux
Dear colleagues,
I want to deposit one structure, but ADIT reports tens more waters
that are further than 3.5 AA away from macromolecule atoms. I
inspected about half of them manually, but all of them are OK. I have
observed this incorrect behavior of ADIT also in one previous
structure for
No.
Some of them have 2.7 AA contacts to main chain!, some of them are in
second, or third solvatation shell. And they are not distributed
around some special area. It is somehow random.
Thanks anyway!
Petr
2011/6/22 Charles Allerston charles.allers...@sgc.ox.ac.uk:
Are they bound to the
Hello All,
I have a covalent link in my structure model that I created using JLigand. I
manually typed the link record in the header information of the pdb file,
however when I refine the structure using this pdb, the output pdb does not
show the link record. Please can anyone help me with
On Wed, 2011-06-22 at 14:10 +0200, Petr Kolenko wrote:
Some of them have 2.7 AA contacts to main chain!
it may be a good idea to report this to the PDB, this seems like a
bug.
--
Hurry up before we all come back to our senses!
Julian, King of Lemurs
In addition to Fred's suggestion, are you certain about your space group ? I
assume you tried phaser with different space groups turned on ?
Another thing to look at maybe the model you are using for MR has some
extensions that lead to clashes in your crystal packing and therefore the
second
dear Subhangi,
have a look at
http://www.ysbl.york.ac.uk/mxstat/JLigand/tutorial_link.html#link
cheers
Stefan
On Wed, 22 Jun 2011 14:04:31 +0100
Subhangi Ghosh subhang...@gmail.com wrote:
Hello All,
I have a covalent link in my structure model that I
created using JLigand. I manually
In my experience ADIT (or ADIT2) is aware of symmetry mates,
and gives a different message for waters related to them- something
about these waters will be moved for you if you don't do it yourself.
I would go ahead and deposit, and when you are given the final file
to OK for release, if it
Dear Petr,
I guess ADIT only looks for interaction between water molecules and the protein
and does not take into account the interactions between water molecules. So if
a water molecule interacts with another water molecule but not with the
protein, ADIT will give you these error report even
Dear Colleagues,
I'm collecting a dataset on our recently repaired Rigaku home source.
Crystal diffracts to 2.2A. Indexing seems to be all fine. However, during
integration, I realize Y-Chi2 is increasing constantly (from 2 to 4.5,
almost linear) within 60 degree collection, whereas X-Chi2 stays
What is your cold stream - phi axis relative and absolute orientation?
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail:
I would like to provide BALBES a set of locally-generated models
to use as MR probes. These files contain SEQRES records and an
arbitrary CRYST1 record
CRYST1 100.000 100.000 100.000 90.00 90.00 90.00 P 1
followed by the usual ATOM records.
I created a subdirectory ./myprobes
containing
The two most likely possibilities are:
1. Beam position changed somewhat after the repair and the site file was
not updated with the new position. This could result in misindexing of the
diffraction pattern with poor positional agreement (Chi2) as a
consequence. The diagnosis of misindexing is
If you make your images available via ftp, I can take a closer look and come
up with plausible explanations and fixes.
Did you lock down the phi-axis?
_
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of bie
gao
Sent: Wednesday, June 22, 2011 11:23 AM
To:
Hi Ethan,
You need to put the files of PDB format in your own database or library.
The error message in get_structure*log shows that BALBES encountered
problems when it started to read your files to prepare the template models.
Thanks,
Fei
On Wed, 22 Jun 2011 10:26:26 -0700, Ethan Merritt
Thanks, Boaz,
That was the problem. Once programs were moved to $CBIN directory they
worked fine through either ccp4i or hkl2map GUI.
Thanks also George and Tim for useful hints.
Huiying
On Tue, 21 Jun 2011, Boaz Shaanan wrote:
They should reside in the $CBIN directory for the gui to see
Dear colleagues
I am pleased to inform that we are organizing an international conference
entitled, “International Interdisciplinary Science Conference (I-ISC, 2011) On
Bioinformatics: An interface between Computer Science and Biology” on 15-17,
November 2011. The purpose of this conference
As a follow up to the excellent suggestions made by others I would suggest
that a close examination of x-file headers may reveal abnormalities in e.g.
crystal orientation -- suspecting an unlocked or drifting goniostat. It may
also indicate a precession around the phi, which should also manifest
23 matches
Mail list logo
