Bill
I've been using 10.5.2 plus the X11 2.1.4 update from the Xquartz
site, I haven't had problems with freezing lately, I _think_ not
since this update. The main problem is that Exposé doesn't work properly
not much help ...
Phil
(looking at a white Easter outside the bedroom window)
1) If I phosphorylate a THR, it comes up with the wrong chirality at
CB. Looking at the dictionary file generated libcheck_TPO.cif,
for some reason it specified it a both chirality which is wrong
TPO chir_02 CB CA CG2OG1 both
Editing this to match THR.cif
TPO
o FEATURE: Active site hilighting. Cheep and cheerful solid
modelling of ligand and neighbouring residues [Herb Klei].
cheep, cheep...
-optionally done now in 0.5.1-pre-1 and following versions.
Paul
Charlie Bond wrote:
How straightforward would it be to modify coot to automatically
'run pdbset' on loaded pdb files to overcome this issue?
Cheers,
Charlie
Lynn F. Ten Eyck wrote:
On 2 Oct 2008, at 09:11, Kay Diederichs wrote:
Phil
On the subject of NCS chains, Paul, I note that you are still using
SSM superposition in determining NCS operators (unless it's been
changed _very_ recently), rather than the LSQ algorithm which would
preserve the sequence register. SSM gets the wrong answer in some
cases, eg in some
As a matter of interest, why do you have to do this? Why doesn't coot
know the Zn is there, it's in the PDB file? Isn't this a bug? : -)
Phil
On 13 May 2009, at 23:45, Paul Emsley wrote:
Moritz Metlitzky wrote:
Hi everybody, i just installed coot and played around a bit with my
structure
why does Coot ignore these atoms renumbered back to 1 beyond 1?
Shouldn't it just ignore the irrelevant atom number?
Phil
On 3 Jun 2009, at 09:19, Kevin Cowtan wrote:
Hi!
Hybrid-36 (initial idea from Ralph Grosse Kunstleve, I think) works
around this problem by allowing higher
OK thanks.
I tried a different example, which did give me a (wrong) assignment -
is there any way of picking an alternative?
What partly confused me before and again was that this command assigns
the sequence but doesn't build the side chains - you have to use the
Ah OK
thanks
Phil
On 4 Jun 2009, at 15:05, Kevin Cowtan wrote:
It's very unlikely to be right on anything much shorter than 12
residues. The confidence scores are a bit gung-ho.
Phil Evans wrote:
OK thanks.
I tried a different example, which did give me a (wrong
Is there a way for Copy NCS residue range to copy to a subset of NCS-
related chains (eg from B to only, not to A D)?
Phil
Be careful how you look at it. As far as I can from trying it here,
the stereo effect is very critically dependent on the vertical
position of your eyes relative to the screen normal (or screen tilt if
you like). Try tilting the screen
Phil
On 8 Sep 2009, at 17:55, Paul Shaffer wrote:
Hi Bill
I just installed this but it seems to have put everything in /Library/bin,
/Library/etc and /Library/lib rather than in /Library/Coot
Is this just me?
Good luck in the struggle
Phil
On 3 Aug 2010, at 02:06, William G. Scott wrote:
Sorry I haven't done this until now. Been
pretty ...
On 4 Aug 2010, at 13:22, Paul Emsley wrote:
On 04/08/10 02:40, William Scott wrote:
Dear Coot OS X people:
Yesterday I put a package on the server that wrongly installed into /Library
instead of /Library/Coot
If you installed it, you can either install the replacement or
If I colour by chain (my preferred option), metal ions disappear
also is there any way of refining a zone around a metal ion without the
sidechains vanishing into the metal density? I know the refine-by-sphere (R)
option works better, but then I have no control over what I'm refining
Phil
On 16 Nov 2010, at 13:22, Paul Emsley wrote:
Dear Phil,
Sorry for the delay, I am only just back from somewhat extensive travels.
On 01/11/10 12:26, Phil Evans wrote:
If I colour by chain (my preferred option), metal ions disappear
Thanks for the notification of this bug. It is fixed
That doesn't work in my OSX coot (maybe an oldish version 3072), no button
appears
The simpler command doe:s
coot_toolbar_button(Sphere Refine, sphere_refine(5.0), reset-view.svg)
Phil
On 19 Nov 2010, at 08:26, Bernhard Lohkamp wrote:
also is there any way of refining a zone around a
This is a coot/refmac problem, but mainly coot I think, and I didn't want to
cross-post.
I'm deeply confused about atom residue naming for nucleic acids.
There are several groups here working with RNA, and I recently broke coot for
them, by installing the latest experimental refmac, and more
Why do you want to quote sigma level anyway? It's more or less meaningless
for the reasons you give. Stick to e/A^3
/flame
Phil
On 22 Dec 2010, at 22:02, Dale Tronrud wrote:
Hi,
I have a crystal structure at 3A resolution with six copies in the
asu. When I average the map over the ncs
/os.pyc
and so on I guess
Phil
On 4 May 2011, at 12:28, Paul Emsley wrote:
On 04/05/11 12:21, Phil Evans wrote:
I've just acquired a new MacBookPro and cloned everything from my old one
across to it, running the same 10.6.7 system
When I try to run coot I get a Python error, see below, both
OK that worked thanks
I'm not sure whether these files got copied over from my old machine - I didn't
do the copy myslef
Phil
On 4 May 2011, at 13:16, Paul Emsley wrote:
On 04/05/11 13:11, Phil Evans wrote:
Is that dangerous?
Not really, python makes the pyc files again (I understand
at 01:16:29PM +0100, Paul Emsley wrote:
On 04/05/11 13:11, Phil Evans wrote:
Is that dangerous?
Not really, python makes the pyc files again (I understand).
Yes, but you're deleting compiled python objects from _system_ directories,
and since normal users can't write to those directories
fault
/Library/Coot/bin/coot-real $@
Phil
On 31 Oct 2011, at 20:03, William Scott wrote:
Hi Phil:
I apologize for not having put it on line. It is now here:
http://sage.ucsc.edu/xtal/coot/coot-0.7-pre-1-628-10.6.tgz
Bill
On Oct 31, 2011, at 6:36 AM, Phil Evans wrote
? eg if Number = 4, then there might be 2 picked residues on either end of
the loop to assume are more-or-less correct (even if not fixed)?
On 30 Jan 2012, at 16:03, Judit Debreczeni wrote:
On 30 January 2012 14:47, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
Can someone explain Extensions
On OSX coot still crashes on adding OXT atoms to C-terminus. This is Bill
Scott's build of 0.7-pre-1 4125 for OSX10.6
This seems to have been a longstanding proble, which I've never seen on Linux
Phil
/usr/local/bin/coot: line 7: 10159 Segmentation fault
/Library/Coot/bin/coot-real $@
(hesitating to restart an old flame war)
There has been a long-standing argument about scaling of electron density maps,
with many people deprecating sigma-scaling, for two reasons
1) in 2Fo-Fc type maps, sigma = RMS density is a function among other things
of the solvent content (smaller with
I'm pretty sure the Aimless fails reported in the nightly builds are OK - I've
changed some things so that you get different numbers
Phil
On 15 Dec 2014, at 18:11, Marcin Wojdyr woj...@gmail.com wrote:
Congratulations!
CCP4 nightly builds also include coot 0.8.1 now.
It's a bigger bundle,
Hi
I've got 4 molecules in the asu (chains A,B,C,D), and have just built a peptide
ligand as chain S on to chain D. Is there an easy way to copy it to the right
position on the other chains, or do I have to put it into chain D?
Phil
In Extensions-NCS-Copy NCS Residue Range the first window asks for the Master
chain, but this seems not to work. As far as I can see, you have to set the
Master Chain in the Draw-NCS Ghost Control window
This looks like a bug, I think
Phil
an xterm. It isn’t a
>> path issue, but some Apple control-freak permission issue, eg:
>>
>>
>> I still haven’t figured out how to get it to work in my normal terminal
>> application.
>>
>> This is some kind of metaphor for what my life has devolved into
Is this a Coot problem or an Xquartz problem?
Just hit this: other things work fine with this Xquartz
Phil
> On 1 Feb 2021, at 19:43, Jason Key wrote:
>
> Hi COOT users,
>
> A message for Mac users of COOT -
> On Friday, XQuartz began prompting users with an update to XQuartz
> 2.8.0_beta1.
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