On Wed, Oct 29, 2014 at 8:53 PM, luzuok wrote:
> I think it is better for COOT to solve this issue.
>
Coot already can be used to solve this issue - I think the automation is
somewhat lacking, but it's vastly preferable to anything involving a text
editor or shell commands.
1. Load molecule
Why? Merging waters like that in coot is a user error, and it does not happen
too often. I realize you are talking about changeable settings, but it would
be really annoying if a refinement program kept removing water molecules that
were placed manually because it does not fit some internal sta
That is a different question- I thought you already knew which atoms are
duplicates.
To identify them, there are programs that will print a list of pairs of atoms
within
a threshold distance from each other.
But in this case I think plain old "sort" program will be easiest.
1. Get all the water
This conversation makes me more and more certain that water update
(add/remove/refine water) done as part of (a default) refinement run is a
good idea -:)
Pavel
On Wed, Oct 29, 2014 at 5:08 AM, luzuok wrote:
> Dear all,
> I found that there are some water molecules in my pdb that share the
Dear Nicolas,
It is really time-consuming! Philip told me to run the structure on PDB
validation server. It will post error if there is duplicate molecules. Then I
can directly find them on a text editor.
I think it is better for COOT to solve this issue.
Best reagards!
Lu zuokun
-
nedit is available in macports.
sudo port install nedit
Best regards,
Blaine
Blaine Mooers, Ph.D.
Assistant Professor
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center Rm. 466
Shipping address:
975 NE 10th Stree
Thanks for the note guys. I really love nedit on my Linux boxes but never knew
that nedit is available for Mac. Can you have the URL for downloading the nedit
for Mac.
Andy
>> Anindito Sen. Ph.D
>> Scientist and Application Specialist in Biological Sciences
>> JEOL LTD.
>> 13F, Ohtemachi Nomura
My guess you might just have to reinstall with the latest version of nedit.
That is what I had to do when I went from 10.5 to 10.9. Have yet to jump to
10.10 yet.
Leonard M. Thomas Ph.D.
Macromolecular Crystallography Laboratory Manager
University of Oklahoma
Department of Chemistry and Bioch
Thank you all for the suggestions.
What worked better for me was to run XDS with different batches of images
and to merge them later with XSCALE.
Best,
Almudena
2014-09-29 11:56 GMT+02:00 Almudena Ponce Salvatierra
:
> Dear all,
>
> I would like to ask something regarding XDS. Is it possible,
Thanks Mark,
that solved the problem.
Thanks also to Ioan, Engin and Jochen, who replied with similar solutions.
Best,
ciao,
S
> On 29 Oct 2014, at 15:56, Mark Brooks wrote:
>
> Try reinstalling X-quartz.
>
> IIRC, /usr/X11R6 is deleted during MacOS upgrades.
>
> Mark
>
> On 29 October 2
Hi,
I think that's a standard X11 library, do you have X11 (XQuartz) installed?
Regards,
Ioan
--
Dr. Ioan Vancea
European Molecular Biology Laboratory c/o DESY
Notkestrasse 85, 22607 Hamburg, Germany
Tel: +49 (0)40 89902-340
Email: ivan...@embl-hamburg.de
On Oct 29, 2014, at 3:45 PM, Sebastian
Try reinstalling X-quartz.
IIRC, /usr/X11R6 is deleted during MacOS upgrades.
Mark
On 29 October 2014 14:45, Sebastiano Pasqualato <
sebastiano.pasqual...@gmail.com> wrote:
>
> Hi folks,
> sorry for the off-topic and slightly ‘demodée’ question, but, since I
> updated to Yosemite on my Mac, "ne
Hi folks,
sorry for the off-topic and slightly ‘demodée’ question, but, since I updated
to Yosemite on my Mac, "nedit" does not work any more.
Here’s the error message:
Seba@host041:~> nedit
dyld: Library not loaded: /usr/X11R6/lib/libXp.6.dylib
Referenced from: /Applications/nedit/nedit
Rea
Dear Lu,
one simple solution is to remove the water molecules with text editor for
example. It depend of how-many times you have multiply water molecules and if
your model have several or more water molecules.
In coot you can remove it graphically, but according to my knowledge not
automaticall
Dear all,
I found that there are some water molecules in my pdb that share the same
position. This maybe cause by merging molecules in coot. It seems that I have
mereged water molecules into my protein for more than one time.
Does anyone tell me how to fix this problem?
Best regards!
Lu Zu
Hi, thanks for all the answers, i will try to wrap up some conclustion once i
have tested things.
Best
Tommi
On Oct 24, 2014, at 7:09 PM, Tim Gruene wrote:
> Hi Tommi,
>
> I used Molscript to place a dotted line in the gap. This shows clearly
> from where to where the gap goes and that the da
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