Hello,
I have 4 molecules.
If I use Phaser's AUTO_MR with all default parameters on them,
I get the following scores:
no_modif remove_H
molecule RFZ TFZ RFZ TFZ
16.9 9.6 7.0 9.4
25.2 5.9 5.4 6.2
34.2 4.5 4.7 5.2
44.9 6.8 5.2 6.7
Hence, here are my e
Markus Rudolph wrote:
Hello,
long ago I had a case when HG1 etc. were interpreted as mercury by phaser.
Could that be relevant to your case?
I hope not.
However, as I have already seen EPMR handle some Hydrogen as Carbon,
I am ready to see anything happening! :(
I will have a quick look to
Just to avoid any problem
pdbcur xyzin X.pdb xyzout X-nohyd.pdb
DELHYD
END
Eleanor
Francois Berenger wrote:
Markus Rudolph wrote:
Hello,
long ago I had a case when HG1 etc. were interpreted as mercury by
phaser.
Could that be relevant to your case?
I hope not.
However, as I have alrea
Dear all,
A bit off the topic question perhaps.
I am trying to find a program which can do multiple structural sequence
alignments. What I would like is a program which can take as input PDB codes
(or files), and which will output a multiple sequence alignment in FASTA format
with the full seq
I ended up using multiprot and staccato recently
http://bioinfo3d.cs.tau.ac.il/MultiProt/
There is a server for multiprot, but I downloaded the applications. I
still ended up doing quite a bit manual editing in filling the gaps in
the structures etc.
I stumbled also over a link about the ma
Hi Jeremiah,
On Sat, Jan 09, 2010 at 05:01:07AM +, Jeremiah Farelli wrote:
> Does anyone know of an example where SHARP was used to phase
> multiple sulphur-SAD datasets and combine all of the data into one
> map?
I'm not aware of exactly such an example - but there shouldn't be any
problem w
Both MUSTANG and MATT are good choices:
http://www.cs.mu.oz.au/~arun/mustang/
http://groups.csail.mit.edu/cb/matt/
On Jan 12, 2010, at 7:17 AM, Ronnie Berntsson wrote:
> Dear all,
>
> A bit off the topic question perhaps.
> I am trying to find a program which can do multiple structural seque
The increase in RFZ is relatively small and not entirely unexpected.
While hydrogens only contribute one electron (as opposed to carbon (6),
nitrogen(7), oxygen(8) and sulfur (16)), there are many hydrogens (in
fact, almost as many as all the other atoms combined). For instance, in
lysozyme you ha
Hi,
When I use the superpose program for SSM alignment with these two structures in
the following command line:
superpose 3BT1.pdb -s B 1OC0.pdb -s B superposed.pdb
The screen output reads:
PDB file 3BT1.pdb has been read in.
... 312 atoms selected using CID 'B'
PDB file 1OC0.pdb has been rea
Hi Ronnie,
the (a) Mammoth tool might also work (but I just tried 6 structures or so when
I used it a couple years ago - not 20).
Jan
--- Ronnie Berntsson schrieb am Di, 12.1.2010:
Von: Ronnie Berntsson
Betreff: [ccp4bb] off topic: multiple structural sequence alignment
An: CCP4BB@JISCMA
Dear CCP4ers,
I think that characterize hydrogens as "transparent" to x-rays is
somewhat misleading. There are plenty of examples where hydrogens are
seen in ultrahigh resolution structures. Modern refinement programs all
use riding hydrogens and it improves models. More precise statement is
Hi all,
When I use the superpose program for SSM aligning these two structures in
the following command line:
superpose 3BT1.pdb -s B 1OC0.pdb -s B superposed.pdb
The screen output reads:
PDB file 3BT1.pdb has been read in.
... 312 atoms selected using CID 'B'
PDB file 1OC0.pdb has been read i
Dear CCP4bb,
since the discussion about H-atoms is on, I wanted to ask about what I saw
during my refinements:
I did refinement with phenix of my 1.9-2.0 Angstroem structures and included
the hydrogens (riding). However, when I checked on the statistics (refinement
close to the end), the avera
Hi Sara,
I don't know what "a good average B" is (or what "a bad average B" is).
I know that the for the refined structure should fall in the
same ball-park range than the temperature factor of the data computed
from the Wilson plot. I am not saying that they should match exactly
though. If
Hi Sara,
- what you observe should not happen since phenix.refine uses riding
model for H atoms. The hydrogen's B-factors are automatically inherited
from the atoms these hydrogens are bonded to. For example, in X-H bond
the B-factor of X should be equal to B-factor of H.
- make sure you are
This server and/or standalone program may be useful as well because of
speed, being that 20 structures will take a while on most servers:
http://ub.cbm.uam.es/mammoth/mult/
At 05:17 AM 1/12/2010, Ronnie Berntsson wrote:
Dear all,
A bit off the topic question perhaps.
I am trying to find a pr
Dear Users,
The deadline for Mar/April 2010 Collaborative
Crystallography proposals will be *January 15, 2009. *
Through the Collaborative Crystallography Program (CC) at the
Advanced Light Source (ALS), scientists can send
Dear All,
January 15, 2010 is the deadline for the March/April 2010 Rapid Access
Proposal cycle.
All Berkeley Center for Structural Biology(BCSB) beamlines are equipped with
ADSC Q315/Q315R detectors, automated sample changers and data collection
software enabling high-throughput crystal screenin
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