Dear all, I know I could use your help to work more effectively so here
comes my questions.
I am building a fairly long polypeptide chain (quite a few hundreds of aa)
in Coot. I got the phases from Phenix, which traced much of the main chains
for me already, with each fragments assigned with
Hi Ed,
Personally I don't care one way or the other, but it may be pointed out
that if D25 is actually number 37 in a homologous protein, it should be
D37. Just as acknowledgement of the (somewhat purist) point of view
that the residue number should denote its linear distance from the
Hi Everyone,
Does anyone have a Zotery style template for Acta Cryst and the like, (s)he
wishes to share? I cannot find it in the repository, but perhaps someone has
made one for private use.
Cheers,
Robbie Joosten
Biochemistry
Netherlands Cancer Institute
Dear Jacob Wong,
have you tried arp warp for model building? It should do a reasonably good job
at 2.3A resolution. Alternatively buccaneer or resolve might also help.
For the overlapping: Does it help to give the subsequent fragment a different
chain ID?
Tim
On Wed, May 04, 2011 at
Hi Robbie
My understanding is that the templates for Acta Cryst. are here:
http://journals.iucr.org/services/wordstyle.html
or here:
http://journals.iucr.org/d/services/latexstyle.html
At least that's what I've always used.
Cheers
-- Ian
On Wed, May 4, 2011 at 8:05 AM, Robbie Joosten
You can use this
http://www.somwhere.org/csl/
to build your style.
Darren
On 4 May 2011 09:05, Robbie Joosten robbie_joos...@hotmail.com wrote:
Hi Everyone,
Does anyone have a Zotery style template for Acta Cryst and the like, (s)he
wishes to share? I cannot find it in the repository,
Thanks Tim for the timely tips. I haven't tried Arp/wARP but will follow
your recommendation right away. I haven't installed Resolve yet but will
look into it and Buccaneer as well - I was having fun modeling some of the
apparent fragments into the density but with a protein so big, I ran
On 04/05/11 14:11, Phil Evans wrote:
Is that dangerous?
If I move it I then get
ImportError: Bad magic number in
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site.pyc
after moving that I then get
ImportError: Bad magic number in
On 04/05/11 12:54, Jacob Wong wrote:
Thanks Tim for the timely tips. I haven't tried Arp/wARP but will
follow your recommendation right away. I haven't installed Resolve yet
but will look into it and Buccaneer as well
I would recommend buccaneer too.
- I was having fun modeling some of the
Hi Ian,
Indeed the word 2007 template is very good (I never got the 2003 version
working well), but it becomes a problem when your co-authors are Mac users with
old Word versions.
Cheers,
Robbie
Date: Wed, 4 May 2011 12:18:59 +0100
Subject: Re: [ccp4bb] Zotero style
From:
Hi Darren,
Thank you for the link. It may be a usefull tool. Unfortunately, the site was
buggy in IE9. It worked much better in FF4, but it stopped when I tried to
generate the final style file.
It turns out that you can also import an EndNote style into Zotero. I tried
this for the .ens
UNIVERSITY OF SUSSEX
An MRC-funded PhD position is available immediately in the Genome Damage and
Stability Centre, School of Life Sciences, University of Sussex. The student
will be supervised jointly by the laboratories of Professor Keith Caldecott and
Dr Antony Oliver, and will
Dear all,
We have solved the sturcture of hen egg white lysozyme
with a barium ion at 2.7 fold data redundancy. Data collected at in-house
copper K-alpha source to 2.22 A resolution with 1 degree oscillation step
per frame. The substructure was correctly identified with just
[switch not too serious mode on]:
well, it is lysozyme, which, according to diffraction properties, should
perhaps be classified as a salt (LyCl7), not a protein... :-)
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3,
UNIVERSITY OF SUSSEX
An MRC-funded PhD position is available immediately in the Genome Damage and
Stability Centre, School of Life Sciences, University of Sussex. The student
will be supervised jointly by the laboratories of Professor Keith Caldecott and
Dr Antony Oliver, and will
UNIVERSITY OF CALIFORNIA SAN FRANCISCO (UCSF)
POSTDOCTORAL POSITIONS, MINOR LAB
Crystallographic studies of ion channels involved in pain and depression
Postdoctoral positions in Ion Channel Structural Biology are available
immediately for highly motivated individuals with a strong interest in
Robbie Joosten wrote:
Hi Ed,
Personally I don't care one way or the other, but it may be pointed out
that if D25 is actually number 37 in a homologous protein, it should be
D37. Just as acknowledgement of the (somewhat purist) point of view
that the residue number should denote its
Can someone return their full path of the location of multilog (used
for browsing dmmulti output)?
I can't find it in my ccp4-6.1.13 installed from Mr Scott's distrib.
Thanks!
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
I made one some time ago (attached). It's not perfect (missing
definitions for e.g. books) but works well for article-references.
-Bjørn
--
Bjørn Panyella Pedersen
Macromolecular Structure Group
Dept. of Biochemistry and Biophysics
University of California, San Francisco
On 2011-05-04
I think that two issues are being confused here. When the anomalous signal
is very weak, e.g. for sulfur-SAD phasing, the anomalous differences are
comparable with the intensity esds. By averaging over many measurements we
can reduce these esds and so improve the signal to noise ratio and the
Hi All,
I have two questions for Pymol.
1. Can you write out the PDB file after structural alignment?
2. How to only show structure that is several angstrom from the ligand?
Thanks a lot in advance!
Eric
1. Yes, just Save Molecule (individually) after align
2. show stick, HETATM around 4
( is your pdb name, 4 = 4 angstrom)
On Wed, May 4, 2011 at 3:26 PM, jlliu liu jlliu20022...@gmail.com wrote:
Hi All,
I have two questions for Pymol.
1. Can you write out the PDB file after
Hi Eric,
On Wed, 4 May 2011, jlliu liu wrote:
Hi All,
I have two questions for Pymol.
the pymol wiki is your friend (http://www.pymolwiki.org/index.php/Main_Page)
as is the pymol users mailing list
(http://sourceforge.net/mail/?group_id=4546). Follow the link to subscribe.
1. Can you
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