Re: [COOT] Coot 0.5 released

[William G. Scott]

Yes, I put coot 0.5.0 into fink cvs, both "stable" and "unstable"  
yesterday. Barring bug fixes, I won't touch the stable entry until 0.6  
is released.


fink selfupdate-rsync

or

fink selfupdate-cvs

I've also built these on my 10.5 machines so they are available as  
fink binary debian packages.




On Sep 24, 2008, at 9:21 PM, Felix Frolow wrote:


Dear Bill it was fast
BTW is it possible to install new coot also via FINK?

Re: [COOT] Coot 0.5 released

[William Scott]

I'm right now making bundles for 10.5 intel and ppc.


You are wonderful! I think you are not told it enough times. I love  
you. Well, in a different way than I love my husband... :-)




OK, with that incentive, they are now ready (for 10.5 so far):





William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/

Re: [COOT] Coot 0.5 released

[William G. Scott]

Hi David:

Here is how I am doing it.  I hope you don't mind that I am cc-ing this.

I picked a directory that I hope will be uninhabited:

/usr/local/xtal/coot

1.  sudo mkdir -p /usr/local/xtal

2.  Download fink's source code and compile it, using /usr/local/xtal/ 
coot as the prefix. You'll need the latest Xcode (3.1 I think) and X11  
(2.3.1).  Use the bootstrap install, and it will prompt you to specify  
the directory.  /sw is the default, but you can tell it to use  /usr/ 
local/xtal/coot


3.  Run the bootstrap.  When prompted, tell it to use unstable  
packages.  When done,


source  /usr/local/xtal/coot/bin/init.sh

fink selfupdate-rsync

fink install coot

You can hack the fftw.info file and remove all references to fortran  
extensions, and that will save about 3 hours of compiling gcc3.4,  
which gives you gfortran, which, as far as I can tell, is useless in  
this context.


I then move   /usr/local/xtal/coot/bin/coot to  /usr/local/xtal/coot/ 
bin/coot.ppc  and then write a wrapper shell script with the line

 source /usr/local/xtal/coot/bin/init.sh
before invocation of the actual coot binary.  This ensures the user  
will have the proper run-time environment but not contaminate the rest  
of his or her setup.  I also modify  /usr/local/xtal/coot/etc/gtk-2.0/ 
gtkrc  to use the aqua -like buttons for the interface.  The  
description of this is in the coot.info file.


4.  Then when it is done, I test it and verify it is working, and then  
tar everything up for next time, and then remove all the spurious  
files and directories, so that the download will be "only" about 120 MB.



Bill




On Sep 24, 2008, at 1:56 PM, David Briggs wrote:


Hi Bill,

happy to help out...

If you can give me a quick bullet point guide to
"not-making-a-mess-of-compiling-coot", then that'd be great.
(What compiler to use, etc.)

A bit new to this, but eager to learn.

Cheers,

Dave

2008/9/24 William G. Scott <[EMAIL PROTECTED]>:

Hi David:

I've got 10.5 covered, and 10.4 ppc (thanks to Luca Jovine!) is on  
its way.


If you would help with 10.4 intel, that would be fantastic.

Bill


On Sep 24, 2008, at 10:51 AM, David Briggs wrote:


OSX 10.4 Intel???

If that's not being done elsewhere, I can volunteer to give it a  
go...


Cheers,

Dave

2008/9/24 Tim Kirk <[EMAIL PROTECTED]>:


We got one here at YSBL.

Let me know what to do and I'll set it doing it.

Given it came from Paul & Kevin's grant from memory it seems only  
fair to

use it this way!

Cheers,

Tim


On 24 Sep 2008, at 16:08, William G. Scott wrote:


Hi Mark:

My 10.4 G4 is lying in a heap of smoldering rubble at work on  
what would
be my dining room table if I was paid enough to own a real  
house, along

with
heaps of wreckage that represent various stages in the life  
cycle of the

SGI
(including some from Alice). (The SGIs, to their credit, still  
work,

even if
there hasn't been an OS update in 10 years.)

I did a security update on my trusty G4, xanana (named for the  
East

Timor
Fretilin rebel leader and subsequent president) and it would not  
reboot.
Apple said it needed a new processor board, which would cost  
more than

an
iMac that is about 10X faster.

So, it is gone the way of the SGI.

I'm right now making bundles for 10.5 intel and ppc.

If anyone has a 10.4 ppc machine and is willing to do this, I  
will be

happy to tell you how. (Basically I just configure a new fink
installation
to build in /usr/local/xtal/coot and then weed out as much as  
possible).


Sorry.  At least it lasted longer than an iPod.

Bill



On Sep 24, 2008, at 7:44 AM, Mark Collins wrote:


you're all quackers :-)

Will somebody be putting a mac G4 10.4 bundle together, for the  
new

version? Please, pretty please!

Mark








--

David C. Briggs PhD
Father & Crystallographer
http://drdavidcbriggs.googlepages.com/home
AIM ID: dbassophile








--

David C. Briggs PhD
Father & Crystallographer
http://drdavidcbriggs.googlepages.com/home
AIM ID: dbassophile

Re: [COOT] Coot 0.5 released

[William G. Scott]

Hi David:

I've got 10.5 covered, and 10.4 ppc (thanks to Luca Jovine!) is on its  
way.


If you would help with 10.4 intel, that would be fantastic.

Bill


On Sep 24, 2008, at 10:51 AM, David Briggs wrote:


OSX 10.4 Intel???

If that's not being done elsewhere, I can volunteer to give it a go...

Cheers,

Dave

2008/9/24 Tim Kirk <[EMAIL PROTECTED]>:

We got one here at YSBL.

Let me know what to do and I'll set it doing it.

Given it came from Paul & Kevin's grant from memory it seems only  
fair to

use it this way!

Cheers,

Tim


On 24 Sep 2008, at 16:08, William G. Scott wrote:


Hi Mark:

My 10.4 G4 is lying in a heap of smoldering rubble at work on what  
would
be my dining room table if I was paid enough to own a real house,  
along with
heaps of wreckage that represent various stages in the life cycle  
of the SGI
(including some from Alice). (The SGIs, to their credit, still  
work, even if

there hasn't been an OS update in 10 years.)

I did a security update on my trusty G4, xanana (named for the  
East Timor
Fretilin rebel leader and subsequent president) and it would not  
reboot.
Apple said it needed a new processor board, which would cost more  
than an

iMac that is about 10X faster.

So, it is gone the way of the SGI.

I'm right now making bundles for 10.5 intel and ppc.

If anyone has a 10.4 ppc machine and is willing to do this, I will  
be
happy to tell you how. (Basically I just configure a new fink  
installation
to build in /usr/local/xtal/coot and then weed out as much as  
possible).


Sorry.  At least it lasted longer than an iPod.

Bill



On Sep 24, 2008, at 7:44 AM, Mark Collins wrote:


you're all quackers :-)

Will somebody be putting a mac G4 10.4 bundle together, for the new
version? Please, pretty please!

Mark








--

David C. Briggs PhD
Father & Crystallographer
http://drdavidcbriggs.googlepages.com/home
AIM ID: dbassophile

Re: [COOT] Coot 0.5 released

[Ethan Merritt]

Congrats on the official release of 0.5

Curious glitch #1:
=

I now get the following set of warning messages on every startup:
/sgpp/local/bin/coot/bin/coot-real: /usr/lib/libGL.so.1: no version information 
available (required by /sgpp/local/bin/coot/bin/coot-real)
/sgpp/local/bin/coot/bin/coot-real: /usr/lib/libGL.so.1: no version information 
available (required by /sgpp/local/bin/coot/lib/libgtkgl.so.5)
/sgpp/local/bin/coot/bin/coot-real: /usr/lib/libGL.so.1: no version information 
available (required by /sgpp/local/bin/coot/lib/libglut.so.3)

I've been running various nightly builds of the pre-release for some time now 
without ever getting a message like this.   I doesn't seem to hurt anything, 
but I'm 
wondering what is the cause.

FWIW I get the same warning message from ldd

ldd /sgpp/local/bin/coot-0.5-redhat-8.0/bin/coot-real
/sgpp/local/bin/coot-0.5-redhat-8.0/bin/coot-real: /usr/lib/libGL.so.1: no 
version 
information available (required 
by /sgpp/local/bin/coot-0.5-redhat-8.0/bin/coot-real)


Curious glitch #2:
==

Hitting the "about" button and selecting either "Coot News" or "About" produces 
the following error trace (again this was working in the pre-release version).

n /sgpp/local/bin/coot/share/guile/gtk-1.2/gtk.scm:
 127: 0* [apply # ()]
In unknown file:
   ?: 1  [#]
In /sgpp/local/bin/coot/share/coot/scheme/coot-gui.scm:
   ...
2279: 2  (let (# # # # ...) (set! text-1 #) (set! text-2 #) ...)
2309: 3* [coot-news-info get-news]
In unknown file:
   ?: 4  (letrec (# # # # ...) (cond # #))
   ...
   ?: 5  [get-news]
In /sgpp/local/bin/coot/share/coot/scheme/coot-gui.scm:
2213: 6  (set! thread (call-with-new-thread get-news-thread 
coot-news-error-handler))
2213: 7* (call-with-new-thread get-news-thread coot-news-error-handler)
/sgpp/local/bin/coot/share/coot/scheme/coot-gui.scm:2213:22: In expression 
(call-with-new-thread get-news-thread coot-news-error-handler):
/sgpp/local/bin/coot/share/coot/scheme/coot-gui.scm:2213:22: Unbound variable: 
call-with-new-thread

Re: [COOT] Coot 0.5 released

[David Briggs]

OSX 10.4 Intel???

If that's not being done elsewhere, I can volunteer to give it a go...

Cheers,

Dave

2008/9/24 Tim Kirk <[EMAIL PROTECTED]>:
> We got one here at YSBL.
>
> Let me know what to do and I'll set it doing it.
>
> Given it came from Paul & Kevin's grant from memory it seems only fair to
> use it this way!
>
> Cheers,
>
> Tim
>
>
> On 24 Sep 2008, at 16:08, William G. Scott wrote:
>
>> Hi Mark:
>>
>> My 10.4 G4 is lying in a heap of smoldering rubble at work on what would
>> be my dining room table if I was paid enough to own a real house, along with
>> heaps of wreckage that represent various stages in the life cycle of the SGI
>> (including some from Alice). (The SGIs, to their credit, still work, even if
>> there hasn't been an OS update in 10 years.)
>>
>> I did a security update on my trusty G4, xanana (named for the East Timor
>> Fretilin rebel leader and subsequent president) and it would not reboot.
>>  Apple said it needed a new processor board, which would cost more than an
>> iMac that is about 10X faster.
>>
>> So, it is gone the way of the SGI.
>>
>> I'm right now making bundles for 10.5 intel and ppc.
>>
>> If anyone has a 10.4 ppc machine and is willing to do this, I will be
>> happy to tell you how. (Basically I just configure a new fink installation
>> to build in /usr/local/xtal/coot and then weed out as much as possible).
>>
>> Sorry.  At least it lasted longer than an iPod.
>>
>> Bill
>>
>>
>>
>> On Sep 24, 2008, at 7:44 AM, Mark Collins wrote:
>>
>>> you're all quackers :-)
>>>
>>> Will somebody be putting a mac G4 10.4 bundle together, for the new
>>> version? Please, pretty please!
>>>
>>> Mark
>>
>



-- 

David C. Briggs PhD
Father & Crystallographer
http://drdavidcbriggs.googlepages.com/home
AIM ID: dbassophile

Re: [COOT] Coot 0.5 released

[Tim Kirk]

We got one here at YSBL.

Let me know what to do and I'll set it doing it.

Given it came from Paul & Kevin's grant from memory it seems only fair  
to use it this way!


Cheers,

Tim


On 24 Sep 2008, at 16:08, William G. Scott wrote:


Hi Mark:

My 10.4 G4 is lying in a heap of smoldering rubble at work on what  
would be my dining room table if I was paid enough to own a real  
house, along with heaps of wreckage that represent various stages in  
the life cycle of the SGI (including some from Alice). (The SGIs, to  
their credit, still work, even if there hasn't been an OS update in  
10 years.)


I did a security update on my trusty G4, xanana (named for the East  
Timor Fretilin rebel leader and subsequent president) and it would  
not reboot.  Apple said it needed a new processor board, which would  
cost more than an iMac that is about 10X faster.


So, it is gone the way of the SGI.

I'm right now making bundles for 10.5 intel and ppc.

If anyone has a 10.4 ppc machine and is willing to do this, I will  
be happy to tell you how. (Basically I just configure a new fink  
installation to build in /usr/local/xtal/coot and then weed out as  
much as possible).


Sorry.  At least it lasted longer than an iPod.

Bill



On Sep 24, 2008, at 7:44 AM, Mark Collins wrote:


you're all quackers :-)

Will somebody be putting a mac G4 10.4 bundle together, for the new
version? Please, pretty please!

Mark

Re: [COOT] Coot 0.5 released

[William G. Scott]

Hi Mark:

My 10.4 G4 is lying in a heap of smoldering rubble at work on what  
would be my dining room table if I was paid enough to own a real  
house, along with heaps of wreckage that represent various stages in  
the life cycle of the SGI (including some from Alice). (The SGIs, to  
their credit, still work, even if there hasn't been an OS update in 10  
years.)


I did a security update on my trusty G4, xanana (named for the East  
Timor Fretilin rebel leader and subsequent president) and it would not  
reboot.  Apple said it needed a new processor board, which would cost  
more than an iMac that is about 10X faster.


So, it is gone the way of the SGI.

I'm right now making bundles for 10.5 intel and ppc.

If anyone has a 10.4 ppc machine and is willing to do this, I will be  
happy to tell you how. (Basically I just configure a new fink  
installation to build in /usr/local/xtal/coot and then weed out as  
much as possible).


Sorry.  At least it lasted longer than an iPod.

Bill



On Sep 24, 2008, at 7:44 AM, Mark Collins wrote:


you're all quackers :-)

Will somebody be putting a mac G4 10.4 bundle together, for the new
version? Please, pretty please!

Mark

Re: [COOT] Coot 0.5 released

[Mark Collins]

you're all quackers :-)

Will somebody be putting a mac G4 10.4 bundle together, for the new 
version? Please, pretty please!

Mark

Re: [COOT] Coot 0.5 released

[Paul Emsley]

David Briggs wrote:

According to Google, Coots make a more "kuck kuck" noise.

2008/9/24 Phil Evans <[EMAIL PROTECTED]>:

 o FEATURE: "Active site" hilighting.  Cheep and cheerful solid
   modelling of ligand and neighbouring residues [Herb Klei].



cheep, cheep...




"kuck kuck" doesn't really capture it... it's more a high pitched and 
loud squawk... as you may discover when sound support is added :)


Paul.

Re: [COOT] Coot 0.5 released

[David Briggs]

According to Google, Coots make a more "kuck kuck" noise.

2008/9/24 Phil Evans <[EMAIL PROTECTED]>:
>>
>>  o FEATURE: "Active site" hilighting.  Cheep and cheerful solid
>>modelling of ligand and neighbouring residues [Herb Klei].
>>
>
>
> cheep, cheep...
>



-- 

David C. Briggs PhD
Father & Crystallographer
http://drdavidcbriggs.googlepages.com/home
AIM ID: dbassophile

Re: [COOT] Coot 0.5 released

[Phil Evans]

  o FEATURE: "Active site" hilighting.  Cheep and cheerful solid
modelling of ligand and neighbouring residues [Herb Klei].




cheep, cheep...

[COOT] Coot 0.5 released

[Paul Emsley]

The Coot Team are pleased to announce the release of Coot-0.5 Ueno.

source: http://www.ysbl.york.ac.uk/~emsley/software/coot-0.5.tar.gz
binaries: http://www.ysbl.york.ac.uk/~emsley/software/binaries/stable
(binaries for other platforms will be appearing in due course).

Paul.




Release 0.5 Ueno

   o FEATURE: Coot now has a Preferences dialog.

   o FEATURE: Coot now is PDB version 3.0 compliant.

   o FEATURE: Additional Representations added [Tadeusz Skarzynski].

   o FEATURE: "Fixed Atoms" for refinement have been introduced.

   o FEATURE: Monomer restraints can be edited in a GUI and are
 exported to the scripting layer.

   o FEATURE: Coot can now make difference maps.

   o FEATURE: The state file now remembers the refinement map number
 [Herb Klei].

   o FEATURE: Add dialog position preferences to Extensions.

   o FEATURE: The state file now remembers the scroll-wheel (contour
 changing) map [Kevin Madauss].

   o FEATURE: Add a variable reduce-molecule-updates-current, that
 when set by the user causes an update of the probed molecule, not
 the generation of a new one [Bob Nolte].

   o FEATURE: Add Terminal Residue now assigns the correct residue
 type (if a PIR sequence has been given for side-chain docking)
 [Bob Nolte].

   o FEATURE: "Pukka Puckers?" validation tool for RNA.  Based on
 Davis et al. (2007) Molprobity: all atom contacts and structure
 validation for proteins and nucleic acids, Nucleic Acids
 Research 35, W375-W383.

   o FEATURE: "Active site" hilighting.  Cheep and cheerful solid
 modelling of ligand and neighbouring residues [Herb Klei].

   o FEATURE: Double-clicking on an atom labels it (CCP4mg
 compatibility).

   o FEATURE: "Eigen-flip" function added.  Use to quickly flip around
 ligands.

   o FEATURE: it is now possible to add a setting so that atoms with
 zero occupancy are not moved when refining:
 set-refinement-move-atoms-with-zero-occupancy [Rajiv Chopra]

   o FEATURE: Refmac can be run from Coot without the user having to
 explicitly set the column labels.

   o FEATURE: NCS Copy Chain is now available as a GUI extension.

   o FEATURE: The ability to turn on chi angles that move hydrogens is
 now available from the Chi Angles dialog.

   o FEATURE: The "About" dialog contains references.

   o CHANGE: Key bindings mechanism has changed.  Now we are able to
 display key binding in a GUI widget.

   o CHANGE: Molprobity Tools (probe and reduce) will only now work
 with those binaries that are hybrid_36 enabled.

   o CHANGE: Picking has been changed to somewhat favour those atoms
 at the front of the slab.

   o CHANGE: When deleting a residue while displaying validation
 graphs, the graphs get updated immediately [JED]

   o CHANGE: In CA display mode, only CAs can now be picked.

   o CHANGE: Nudge centre axes are now relative to the screen rather
 than in world coordinates.

   o CHANGE: NCS skipping changed.  Hopefully faster now [Steven
 Sheriff].  Also works in the case of hetero dimers with NCS [Phil
 Evans].

   o CHANGE: default bond width changed to 5.

   o CHANGE: Traffic lights verticalized.

   o CHANGE: Symmetry colour info added to state file [Doug Kuntz].

   o CHANGE: the argument order for "mutate" scripting function
 have been canonicalised.

   o CHANGE: set-symmetry-colour-merge now takes only a fraction
 argument.

   o CHANGE: Mutate no longer changes the atom order in the pdb file.

   o CHANGE: Next Residue/Previous residue reworked so that it now
 jumps over gaps and goes to the right residue when encountering
 insertion codes.

   o CHANGE: Don't allow translation drag of intermediate atoms during
 rotamer selection.

   o CHANGE: Reference structures now have strand markup in the
 header, so they can now be used as the reference structures for
 "Build Strand".

   o CHANGE: Bond parameters changes (bond width and hydrogens state)
 now work immediately, no need to press the "Apply" button [FvD].

   o CHANGE: Colour by Chain style also now displays zero occupancy
 markers [PRE].

   o CHANGE: Modelling toolbar can now be removed or docked in
 different positions.

   o BUG-FIX: chiral volumes are now correctly handled for multiple
 monomer bespoke ligand dictionaries.

   o BUG-FIX: Hydrogens names are better handled after an undo
 operation - no longer do they fly off when refining [Joel Bard]

   o BUG-FIX: Non-flexible ligands can be added to ligand search when
 the "flexible?" option is selected.  Previously the ligand search
 was aborted.

   o BUG-FIX: Flexible ligand fitting when the torsion period is 0 and
 for ligands that have bonding defined from a cif file (no atom left
 behind).

   o BUG-FIX: side-by-side stereo mode improved [Randy Read].

   o BUG-FIX: Now coot does not crash on when displaying NPD atoms
 in anisotropic representation [Mitch Miller