Hi Jared and all,
There is also a JAVA program called PDBeditor by Jonas Lee that may make the
PDB editing part a little easier or less error prone:
http://sourceforge.net/projects/pdbeditorjl/
I did a little test and find it pretty useful, especially for those who do not
have access to a text
Thanks to Paul and Zhijie for the suggestions.
In the past, I’ve also renumbered everything from 1 (using pdbset) for the
duration of refinement, then renumbered the structure at the end. For that, I
would use either pdbset and a text editor (which is somewhat tedious, as there
are several
Thanks to all. I noted down all the information you shared with us.
Cheers!
Johnson L.W
On Tue, Jan 13, 2015 at 3:08 PM, Valerie Biou valerie.b...@ibpc.fr wrote:
hello
we have a French press, a bead machine and constant CellD disruptor in our
institute. I can tell you that most people
Have you done it?
1) Click “add residue...”
2) Click that “real space refine zone” button.
You will see what will happen.
From: Dialing Pretty
Sent: Wednesday, January 14, 2015 9:24 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Coot: How to connect N-terminal to neighbouring C-terminal
Dear
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Dear Dialing,
in that situation you only see the residues unconnected because they
are too far apart. The refinement suggested by Zhijie Li would bring
them in proper distance.
Best,
Tim
On 01/14/2015 03:24 PM, Dialing Pretty wrote:
Dear All,
Dear Dialing,
Just in case, make sure you get the residue numbering right. I.e., if you are
try to insert a new residues between two residues already consecutively
numbered, for example 96-97 or 134-135, then Coot will not to create the
connection with the new residue.
HTH
D
-Original
Dear All,
Suppose I delete a residue ( residue 100 for example) for outlier refinement,
then I add the same residue at the C-terminal of residue 99 (by Add terminal
residue function of the Coot). By coot, how can I connect the C-terminal of
residue 100 to the N-terminal of residue 101?
I am
If the residues are consecutively numbered (Calculate Renumber residues),
and are assigned the same chain ID (Calculate Change Chain ID), Coot
might surprise you and link them on its own.
On Wed, Jan 14, 2015 at 9:39 AM, Zhijie Li zhijie...@utoronto.ca wrote:
Have you done it?
1) Click
Mintu,
Can you be a little more specific about what your problem is? Are you
worried about the rfactors (they don't seem too bad) or the lack of
secondary structure?
Regarding the secondary structure - some proteins just don't have much! As
long as the fit to density and geometry are good, I
Hi Jared,
The only thing that comes to my mind that might help a little is to use pdbset
to renumber your residues. Then you only need to change residue 101 to 100A
manually in a text editor (unfortunately I could not find a program that does
that).
Here are the steps I would take:
1) build
Hi Randy,
Thank you very much for the advice. I use CCP4 version 6.4.0 on my Mac OS X
10.10.1, after my updating my Mac OS X to 10.10.1 three weeks ago, I did
have a issue to open CCP4, I have to re-install X-Quartz and after that I
can open CCP4 well. I haven't updated CCP4 to 6.5, maybe I should
Hi Evans,
Thank you very much for the suggestions! I'll post my data on an online
file sharing system from now on.
Xiao
On Tue, Jan 13, 2015 at 5:21 AM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
It is hard to tell without having the unmerged data (don't post that to
the BB), but running the
Hi Vaheh,
Thank you for point out this. You are right, the crystal is a plate and
somehow at certain angles the frames even failed index, I see a lot of
rejection spots when integration. From all the suggestions I got so far, I
think I have to grow better crystals and try better collecting data
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Hi Jacob,
both George Sheldrick and Andrew Leslie explained to me that the
machine I had in mind - a sealed tube generator with a graphite
monochromator - is not really state of the art and merely a technology
from 20 years ago. Hence my comment
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