Hello Hyunchul Kim,
I found this paper very interesting:
Novotny M, Seibert M, Kleywegt GJ.
On the precision of calculated solvent-accessible surface areas.
Acta Crystallogr D Biol Crystallogr. 2007 Feb;63(Pt 2):270-4. Epub 2007 Jan
16.
PMID: 17242521 [PubMed - indexed for MEDLINE]
Hello Miguel,
Thank you for your reply.
It's related to the total SASA of a protein structure but not that of
per residue. However, it still give me a hint. :)
Best,
Hyunchul Kim
On Tue, 2007-07-24 at 08:12 +0200, Miguel Ortiz-Lombardía wrote:
Hello Hyunchul Kim,
I found this paper very
Registration for the 21st Rhine-Knee Regiomeeting 2007 in Hölstein (CH)
is open until August 31th, 2007 under
http://www.bioc.uzh.ch/index.php?204L=1 .
Best regards,
Peer Mittl
Yes, that is our intention. CCP4 would probably be at the third level of
a hierarchy including:
Macromolecular crystallographic techniques
Structure solution, analysis and visualisation software
The CCP4 suite
So there would be room for other software packages at the same level as
Hi Hyunchul Kim,
the paper that Miguel quotes concludes that the ASA doesn't show any
correlation with resolution, but i would like to respectfully disagree. In the
paper, the authors limit themselves to structures determined at a resolution no
lower than 2.3 A. Many complex structures though
Date: Tue, 24 Jul 2007 11:49:35 +0100
From: Stephen Brian Carr [EMAIL PROTECTED]
To: ccp4bb@jiscmail.ac.uk
Subject: mosflm error
Message-ID: Pine.VMS.3.91-2 (vms)[EMAIL PROTECTED]
MIME-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
Dear ccp4bb-ers,
I have started encountering an error
Thanks for the replies so far.
Here is some more information I should have included last time.
The COORDS file is being written, but mosflm seems unable to
read it. The simple things like the file permissions are all correct
and there is plenty of free space on the disk.
Thanks again
Hi Rob, Hyunchul Kim and Miguel,
I was just about to write a comment on this, but Rob was quicker..
Rob is right, our dataset of hen egg-white lysozymes does not contain
any structures with resolution lower than 2.3 Aone may say that
these are all relatively high-resolution structures,
I am working with a small protein in a relatively high
space group p6322 and have good data to a modest 2.5 A
resolution. During the first rounds of restrained
refinement however the B factors drop to an average of
15 and as low as 2 A^3. This has the effect of
producing large amounts of
Hello all,
I have a coordinate file of an energy minimized molecule which was
apparently done using Chem 3D Pro. Does anyone know how I can convert
this to a pdb file?
Thank you
Mona Rahman
--
Mona N. Rahman, Ph.D.
Post-doctoral Fellow
Botterell Hall, Room 634
Department of Biochemistry
Thank you for the help. It seems as if the new Refmac5 has done the trick.
Thanks
Craig
Craig McElroy, Ph.D.
Department of Molecular and Cellular Biochemistry
Ohio State University
483 Hamilton Hall
1645 Neil Ave.
Columbus, OH 43210
(614) 688-8630
Anastassis Perrakis wrote:
Hi there -
That
Hello Mona,
I am guessing you have the atom name,number and coordinates in your file.
I did something like that and Openbabel will convert it to the pdb file
you desire but as far as I know, you will have to assign a residue name to
the atom yourself. I did this by superimposition on the original
Thanks for the advice everyone. I downloaded the graphic interface for
Open Babel but for some reason it's not converting my file. I'll play
around more with this later but any hints would be greatly appreciated.
On Tue, July 24, 2007 09:50, Seth Horne wrote:
Try Open Babel at
First, Thank you all for the help and suggestions, it
truly resolved the issue.
First I reset the B factors to something close to the
Wilson B average (53). Then making sure the
B-solvent contribution flag was set and refining
isotropic b-factor I reran the job. The B-factors now
are
[EMAIL PROTECTED] wrote:
Hello Mona,
I am guessing you have the atom name,number and coordinates in your file.
I did something like that and Openbabel will convert it to the pdb file
you desire but as far as I know, you will have to assign a residue name to
the atom yourself. I did this by
Thanks to all those who responded. Here is a summary of the
responses. Overall,
there are mixed feelings, but there is a clear bias towards Akta, with a
better service and durability – individual experiences with service might be
due to geographical distributions?
Filip
Hi,
I have an mtz file from Phenix I am trying to convert for use in Refmac. The
labels are currently:
H
K
L
I-obs
SIGI-obs
R-free-flags
I can't seem to get it to work. I am using Import, it runs, spits out a new
mtz, and then Refmac complains about the labels. What is the easiest way (ie
Use truncate to convert I-obs to F-obs. No format change is needed.
Peter
John Bruning wrote:
Hi,
I have an mtz file from Phenix I am trying to convert for use in
Refmac. The labels are currently:
H
K
L
I-obs
SIGI-obs
R-free-flags
I can't seem to get it to work. I am using Import, it
Since I was reading it this afternoon again, I cant help but suggest
to all refinement newbies and more experienced 'refiners' my favorite
read:
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2156-68.
Epub 2004 Nov 26.
Introduction to macromolecular refinement.
Tronrud DE.
You might need to make sure that the input format you are entering is the
correct one for the program that created the file.
Thanks for the advice everyone. I downloaded the graphic interface for
Open Babel but for some reason it's not converting my file. I'll play
around more with this
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