Re: [COOT] to separate levels of positive and negative density

[chern]

Hi all,
Is it possible to separately adjust the levels of positive and negative 
electron density? When I try to build a fragment with a poor density I want 
to decrease the level of positive density from 3 sigma to 2 or even 1 sigma 
to see more positive density, but then the whole map becomes red with 
negative density. Can I shut off the negative density at all, leaving only 
the positive density in the PHFOFCWT maps? ( I would like also to color them 
separately). It is possible to do so in xtalview.


Maia

Re: [COOT] Novel maps...

[chern]

Dear all,

Thank you  for your help with occupancies.

Maia


- Original Message - 
From: "Paul Emsley" 

To: 
Sent: Tuesday, June 23, 2009 9:38 AM
Subject: Re: Novel maps...



>

Maia Cherney wrote:

Hi all, Is it possible to change residue or atom occupancies in coot?

Maia



Yes.


http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC147

Re: [COOT] Mac version of coot

[chern]

Hi,
I am trying to find the latest version (0.6) of coot for Mac with nice 
icons. Is there such a version?


Maia



- Original Message - 
From: "Paul Emsley" 

To: 
Sent: Tuesday, June 23, 2009 9:38 AM
Subject: Re: Novel maps...



>

Maia Cherney wrote:

Hi all, Is it possible to change residue or atom occupancies in coot?

Maia



Yes.


http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC147

[COOT] Ramachandran plot

[chern]

Hi Paul,
I don't understand the changes in the Ramachandran. plot when I click on it. 
I see movement of allowed regions. Could you please explain that movement, 
what it means?


Maia 

Re: [COOT] garbled terminal output

[chern]

Hi,
I saw garbled terminal output many times. When it happens, I usually close 
Coot and start it again from a new terminal.



- Original Message - 
From: "Kevin Cowtan" 

To: 
Sent: Thursday, December 17, 2009 8:23 AM
Subject: Re: garbled terminal output



This happens to a terminal when it trys to display ascii code 14
(ctrl-N), which switches the display to the top 128 ascii characters.

To check this, save the attached text file and then cat or more it from
a terminal. It should have the same effect. (In a gnome terminal, you
can do Terminal/Reset to restore it.)

Now, I've never seen this happen for anyone else. So I'm guessing there
is something in your saved session or config files which is causing this
to happen. We might be able to work out what if you can send the full
coot log output.

If you do

coot >& coot.log

and wait for the program to start up, then quit and mail the log file,
then that might provide some more clues.

Kevin


Paul Emsley wrote:

Ben Eisenbraun wrote:

Hi Cooters,

I have a user running Coot from the official binaries (coot-0.6-pre-1-
revision-2486-binary-Linux-i386-centos-4-python-gtk2) on Red Hat Linux
4.6.

Using Gnome Terminal, when coot runs, the shell output is garbled.  It
looks like this:

(⎽␊├-⎽≤└└␊├⎼≤-␌⎺┌⎺┤⎼  0.10  0.20  0.80)
(⎽␊├-⎽≤└└␊├⎼≤-▒├⎺└-┌▒␉␊┌⎽-␊│⎻▒┼␍␊␍ 0)
(⎽␊├-▒␌├␋┴␊-└▒⎻-␍⎼▒±-°┌▒± 1)
(␤▒┼␍┌␊-⎼␊▒␍-␍⎼▒┬-└⎺┌␊␌┤┌␊-┬␋├␤-⎼␊␌␊┼├⎼␊
"/┤⎽⎼1/≤±⎺┌␍±┤⎼/␋┼├␊±⎼▒⎽␊/1BIS.⎻␍␉" 1)
R␊▒␍␋┼± ␌⎺⎺⎼␍␋┼▒├␊ °␋┌␊: /┤⎽⎼1/≤±⎺┌␍±┤⎼/␋┼├␊±⎼▒⎽␊/1BIS.⎻␍␉
 PDB °␋┌␊ /┤⎽⎼1/≤±⎺┌␍±┤⎼/␋┼├␊±⎼▒⎽␊/1BIS.⎻␍␉ ␤▒⎽ ␉␊␊┼ ⎼␊▒␍.
S⎻▒␌␊±⎼⎺┤⎻: P 1
C␊┌┌: 45.09 45.08 49.43 68.82 64.74 62.63
INFO:: F⎺┤┼␍ 1 └⎺␍␊┌⎽
   M⎺␍␊┌ 1 ␤▒␍ 0 ┌␋┼┐⎽
S≤└└␊├⎼≤ ▒┴▒␋┌▒␉┌␊ °⎺⎼ ├␤␋⎽ └⎺┌␊␌┤┌␊
INFO:: NCS ␌␤▒␋┼ ␌⎺└⎻▒⎼␋⎽⎺┼ 146/226

Coot sets LANG=C in the coot start up script, so I don't think it's a
character set issue per se.  It _doesn't_ happen on a build of revision
2439, so some change in between 2439 and 2486 seems to be causing this.
I went through the commit log on Google Code, but didn't see anything
obvious.

If the user does a hard reset of Gnome Terminal, it apparently fixes the
issue, and it's happening on multiple machines in their lab.

To add another data point, if we capture stdout to a file and view the
file, the text looks normal.

Uh, any ideas?  I'm mostly out at this point.



Hi Ben,

I don't know what could have happened between those revisions. Please
try adding to you ~/.coot

(set-console-display-commands-state 0)

or perhaps

(set-console-display-commands-hilights 0 0 0)

Paul.
















Re: [COOT] Unmodeled blobs behaviour

[chern]

Yes, I have this problem, too.


- Original Message - 
From: "Paul Emsley" 

To: 
Sent: Monday, April 26, 2010 12:36 PM
Subject: Re: Unmodeled blobs behaviour



Jan Dohnalek wrote:


I have noticed that Coot puts me in irrelevant places when I use the 
Unmodeled blobs validation. It does its job but then the list of blobs 
sends me to perfectly interpreted places and I cannot see any 
uninterpreted blobs...


I don't know why this should be, I have not seen it before.

Paul.

[COOT] coot installation

[chern]

Hi,

I would like to install ccot on my laptop. I have a linux vmvare with 
mandrake 10.1 OS and i686 kernel.

Which tar should I use?

Maia