mean 0.3.3 not 0.0.33
and apparently none of them allows this.
That indeed is the case. Not sufficiently modern.
Try a recent 0.5-pre release and look out for Fixed Atoms.
Paul.
Thanks in advance for your replies.
Ricardo
From: Paul Emsley
Date: Tue Nov 21 2006 - 17:58:19 GMT
On Tue
In message [EMAIL PROTECTED]
[EMAIL PROTECTED] writes:
Hello
I would like to rotate/translate a multi-subunit complex, each subunit
having a different chain name. Is there a way (maybe a script) that allows
this to be done in Coot without attempting to change to a single chain
name?
I
Mark Collins wrote:
Dear Coot Community,
I'm having a few issues installing/running Coot 0.5-pre osx ppc. I
have a G4 Powerbook and G4 mac mini, both running 10.4.
First the powerbook and mini were hanging with the start (coot) image
and the startup log says:
...(looks normal).
There
William Scott wrote:
The Apple X11 guy is now working with coot
interesting..!
to try to fix the bug that causes it to freeze or crash, and there
will likely be a new release soon. The problem is beyond my very
limited abilities, I am afraid.
So start the download and then go to the pub.
Nian Huang wrote:
Dear all,
After putting a ideal double-strand DNA around density, I found it is very
hard to move both chain together. Using rotate/translate zone only results
in single chain movement. Is there a function in coot that can
rotate/translate a whole molecule in an easier way?
Mark Mayer wrote:
Hi Cootaners,
Anyone know if its possible to redefine the default Z location for the display in hardware stereo
mode? The default value seems to be the plane of the stereo window, and although I can move the
plane deeper into the window with control/right-mouse-drag, when I
William Scott wrote:
(set-bond-thickness 0 3)
works
but the menu-driven option for me doesn't anymore.
Bug?
Yes, bug.
The workaround (that works for me) is to activate the default molecule.
That gets it unstuck.
Paul.
jenny flower wrote:
Hello,
I have 4 chains in my pdb, I SSM chain B,C,D to chain A. If I refined
chain A, can regenerate a pdb with whole 4 chains from refined chain A,
by applying SSM matrix? I see Xterm window show SSM matrix when I do
SSM, but somewhere a log file contain this matrix
to chain A, so seems
it wouldnot work by apply NCS. Now I would like to run refmac5, so I
need a complete model, right?
I am a rather beginner, is there any better ways to rebuild in my case(4
molecules in one assymetry unit).
thanks
On Sun, Aug 10, 2008 at 9:36 PM, Paul Emsley [EMAIL PROTECTED
nihmmayerm wrote:
Hi,
The problem was that coot choked on the TER and BREAK lines in the PDB,
once I removed these 0.4.1 reads the phenix PDBs fine.
Hmm... where, I suspect, choked on means parse according to the
definition. I have not heard before of a BREAK card and AFAICS, it is
not
Evan Kantrowitz wrote:
I am now using an autostereoscopic display (no 3D glasses required) from DTI
Technologies. I have been using this display with PyMol and the stereo is great. There is
essentially no eye strain and no flicker at all.
It does not work correctly with COOT since it
Evan Kantrowitz wrote:
Yes, when you use the side by side in COOT with the autostereoscopic display the molecules
are too fat by a factor of 2.
You can try this:
(set-dti-stereo-mode 1)
Paul.
Dear Cooters,
I have had reports that in certain circumstances, only the top
molecule is clickable - which I am sure can be annoying. However, I
have not been able to reproduce this here.
So, if you are suffering in this way, please tell me which coot binary
tar file you used (and anything
Janesh wrote:
Hi,
I am having problems executing the NCS EDIT command...
I have 2- fold NCS and want to apply the edits from CHAIN A as my master molecule to
the B chain. I am using the command following command which is not working...
copy-residue-range-from-ncs-master-to-others 0 A
either
I wonder if Chrisitan has a different definition of quick and easily...
To trim[1] atoms that are below a given map level see Section 6.15 of
the user manual:
http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_6.html#SEC170
[1] delete or set to zero occupancy.
Paul.
Dirk
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
Leonardo Castro Palmieri wrote:
Congratulations for the great software!
Thank you - appreciated.
Will be a 64 bits version of coot 0.5 released?
Yes... in due course. I'll need to acquire a 64 bit machine/OS to build
the nightlies on.
I intend now to deal with matter arising from
Another remark on colours in 0.5: redhat8 (non-pythonic) binaries on RHEL4 seem to have lost colours --
the model/fit/refine window, scripting window etc are all grey.
Dear Judit,
Oh I see.
It's a gtk1 vs gtk2 problem:
Please replace your xxx/share/coot/cootrc with the one in:
Nobuo OKAZAKI wrote:
Dear Coot 0.5 users
I'm using coot 0.5 (redhat8 binaries) on Vine Linux 4.2 (Japanized linux
based on redhat 8 or 9). In this version, Edit chi angles lost green
indicator for target bond.
Yes, sorry. This problem means that 0.5.1 will be needed :-/
Paul.
Ricardo Leal wrote:
Dear Coot Mailing list,
I am using wincoot 0.5 pre (downloaded 1-2 months ago) and I am having
problems writing hydrogens (I am refining neutron data) to the output pdb
file. Basically coot eats the double prime.
Dear Richardo,
You need a fresher Coot.
Giles Robertson wrote:
Dear folks,
Just wanted to point out that in version 0.5 (and older) the cis trans
isomerism gets messed up when reading in the smiles code for a small
molecule. For example C/C=C/C looks the same as C/C=C\C. Although
it is possible to edit the .cif file manually, I
It turns out that Eugine Krissinel is way ahead of me - in mmdb he
provides a flag to fix up the missing elements.
This is non-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
Les Tari wrote:
I realize that I left out a key detail, and had a typo on my last post. I am running Coot 0.5
on OSX (intel). The error message I see when I try to refine a monomer I generate with the
CCP4 monomer library sketcher that there are NO restraints found for the ligand (despite
the
S. Shanmuga Sundara Raj wrote:
Is there a way to export the environmental distances to a text file?
These distances are not saved in the saved state (*.scm). Can you save
the session with the environment distances?
Not exactly, but you can find the residues that are close (5.5A say) to
a
Lieven Buts wrote:
Hello all,
I have just been experimenting with the refinement options for twinned data
in phenix.refine (final 1.3 version), and I ran into a strange problem with
the density fit validation function in Coot 0.4 and 0.5. When I auto-open
the MTZ file with map coefficients
In message [EMAIL PROTECTED] Paul Emsley
[EMAIL PROTECTED] writes:
Hi Mark,
The issue here is that the dictionary does not define those atoms for e.g. ARG
and GLN.
For ARG and GLN, the atoms bound to the CG are HG1 and HG2 - not Hx3.
i.e.
Coot doesn't know about bonds to those atoms
Yes it should. :-(
Paul.
In message [EMAIL PROTECTED] junfeng liu [EMAIL PROTECTED]
writes:
It worked well on old versions. For coot 0.5,it works when you restart
coot or overlap small fragment on big one sometimes .
That should be a bug. Is it right Paul?
Best wishes!
liu
Engin Ozkan
James Whittle wrote:
Hi-
I'm trying for the first time to work with a structure in spacegroup
H32. Coot reads the CRYST card, but when I build a helix, or look at a
H32 PDB entry, the symmetry mates appear squished. I know there is some
discussion about handling this spacegroup: do I need to
Eleanor Dodson wrote:
Paul Emsley wrote:
James Whittle wrote:
Hi-
I'm trying for the first time to work with a structure in spacegroup
H32. Coot reads the CRYST card, but when I build a helix, or look at
a H32 PDB entry, the symmetry mates appear squished. I know there is
some discussion
Dear Richard,
Richard Kingston wrote:
Working with Coot 0.5 revision 1444, I'm seeing strange behavior reading
and writing files for Shelx
If I simply read in the shelx .res file, then write a .ins file straight
back out, the anisotropic B coefficients are changed.
An example ...
Read
FYI, IIUC, Morten Kjeldgaard has become a MOTU and is working on
crystallographic libs for Ubuntu, e.g.:
https://launchpad.net/ubuntu/+source/clipper
https://launchpad.net/ubuntu/+source/mmdb
When he gets round to Coot I'm keen to help make his life easier.
Regards,
Paul.
Mark Brooks
Taufik Al-Sarraj wrote:
Hello everyone,
I am new to Coot, I am trying to do a DNA mutation but unfortunately i
have not been successful. I am using Mutate Residue Range.
The error message i get is
'INFO:: mutate 2 to a ALA
DISASTER! Not all necessary atoms found in residue 2
CA is missing
Aengus Mac Sweeney wrote:
Can coot deal with PDB files that have residues numbered 100A, 100B, 100C
etc?
I can't find a way to make rotamers or auto fit rotamers work for these
residues.
Hi Aengus,
My initial answer to this was of course! - now I tested it and and I
think oh dear. High
Sang wrote:
I am running Coot 0.5.0-1 on Mac OS X 10.4.11 (Dual 2.7 GHz Power PC G5, 2
GB DDR SDRAM), which was installed with fink. ccp4 is 6.0.2-7, again
installed with fink.
when I want to get monomer, it freezes quite long time (more than 5 min) to
write cif file using refmac. the monomer I
We are pleased to announce the release of Coot-0.5.2.
This is mostly a bug-fix release (of 0.5/0.5.1) but a few new features
sneaked in too.
source:
http://www.ysbl.york.ac.uk/~emsley/software/coot-0.5.2.tar.gz
binaries:
http://www.ysbl.york.ac.uk/~emsley/software/binaries/stable/
Thanks,
junfeng liu wrote:
Dear All,
I am overlaying several structures using coot. There are two ways SSM
or LSQ can be used in that package. But I got clearly different
result form the two methods. In my opinion SSM only works on the
secondary structures and LSQ can works on the whole atoms
Hi Ben,
Ben Eisenbraun wrote:
I seem to be running into the same problem reported by other people with
Coot showing a blank clashes window.
I'm using the official Coot 0.5.2 python-gtk2 binary on Fedora 10 with
probe 2.12 and reduce 3.13. Probe/reduce seem to run correctly; I get a
In message 4964b4e6.4000...@ysbl.york.ac.uk e.dod...@ysbl.york.ac.uk writes:
At present the only way to calculate an E map via the input option to
read an MTZ file is to redefine the COLUMN type of E to that of F
Bleugh.
Could this be fixed please?
Certainly.
Paul.
Pete Meyer wrote:
Using molprobity 3.15 with coot 0.5.2 (gtk1 on ubuntu 7.10 amd64), the
dialog box that results from running the molprobity-produced script has
overlapping buttons (so problems in one residue are masked by problems
in another).
Does anyone have any ideas if this is a molprobity
Pete Meyer wrote:
schemic:
(set-default-temperature-factor-for-new-atoms 37)
http://www.ysbl.york.ac.uk/~emsley/coot/doc/doxygen/html/c-interface_8h.html#a436
It does appear that this approach doesn't work (at least for adding
terminal residues using 0.5.2).
You are quite right - my
Oliver Clarke wrote:
That works very well, thanks Judit, and thanks to Paul for the initial
script.
Is there a way to give refine-zone a list of residues rather than a
range?
No. There will not be.
refine-residues doesn't seem to adopt the restraints I set in
refine/regularize control
Dear Cindy,
cindy wrote:
I am running Coot 0.1.1 on an SGI.
Ah, I am getting forgetful about how things worked in 0.1.1
I'm trying to incorporated methylated lysines into my model, but it is not working. I've
done the following
File=Get monomer
placed the methylated lysine where I want
Roger Rowlett wrote:
I am experiencing a strange Coot crash issue on some of my Linux
workstations. Coot 0.5.2 or 0.6-pre1 crashes with an identical failure
mode with the following Coot output (last few lines):
[...]
load tips.scm
load americanisms.scm
load group-settings.scm
Schubert, Carsten [PRDUS] wrote:
Would it be possible to enhance the Change Chain ID.. function to
allow for insertion of residues into an existing chain if the given
resid range is not occupied?
if you use the Use Residue Range option you can do this.
Could the function be modified in
Engin Ozkan wrote:
Hi, it's me again.
With the latest version (1848), I haven't been able to use
rotate/translate or rigid body functions (they were fine in 1847, I
think). No matter what I set it to, the whole chain gets moved by these
functions
:-( Yes I do too. Will fix.
hari jayaram wrote:
I have a low-ish resolution (3.5 ) map for a membrane protein. I have
been using helical restraints heavily in pymol to do the model building
(versions 0.4.2 to 0.5.1 to 0.6 pre release ) . The structure is very
homologous to something else and these are really long
Jianghai Zhu wrote:
Hi,
The new version of coot has o key binds to other NCS chain, which is
a great shortcut. It works perfectly between my A and C chains.
However, it won't work between B and D chains and gives me the following
error.
(skip-to-next-ncs-chain)
((safe_scheme_command)
First: good.
Second: a technical note: recently I discovered that many (most?)
consumer graphics cards do not support GL_LINES [1] for line widths
other than 1 pixel - they simulate them using OpenGL quads
(quadrilaterals), so it is not completely surprising that somehow the
simulation was
Garib Murshudov wrote:
Have you declared your modified LYS as L-peptide. It should be be done
in the beginning like:
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
Kay Diederichs wrote:
David Schwefel schrieb:
Dear Coot community,
I encountered some problems using Coot on fedora core 10. I installed
the
binaries, and upon starting, the system crashed just in the moment
when the
Coot window appeared. I have a ATI radeon X1650 graphics card. When I
Victor Alves wrote:
Hi
I have looked at the reference manual and can't seem to find a way to
fulfill my desire to change colors of the active map or molecule at
key-press.
All the commands I found use imol which means you have to know the
exact number. If you're launching Refmac from
Schubert, Carsten [PRDUS] wrote:
Yep it does. On linux there may be issues, because the drivers may or may not
support swap-eyes. The problem is that the images are out of sync with the
glasses, or to be more precise, the left image is displayed when the right
shutter on the glasses is open.
Markus Dehnhardt wrote:
Dear cooters,
I am new to coot, but I have already discovered how powerful
extensions and key bindings can be. My question is quite simple: if
I want to generate my own extension or keybinding, which scripting
language is better suited? I am not very familiar with
Jhon Thomas wrote:
Hello paul
I am completley naive with coot.I am using the coot present with the
ccp4-6.0.2, which is an older version of coot. I am facing very
difficulty in optimising the geometry of the model in coot.I follow
the tutorial for optimisation of the geometry. i go like
Meindert Lamers wrote:
Dear all,
I was wondering if there is a way to open the following windows using a
startup script.
-Cell symmetry
-Stereo/mono
-Refine regularize control
-Bond parameters.
No, no [1] , no and no.
But they would be useful to add - along with the scripting window.
Bottomley, Matthew wrote:
Dear Cooters,
Is WinCoot able to handle glycosylated Asn residues? If I load my
current PDB file that contains an Asn with an N-linked NAG modification
the NAG does not appear bonded to the Asn side-chain (whereas in Pymol
this connection is drawn). The Asn and NAG
Cathy Lawson wrote:
I'd be grateful for a short click-by-click description of how to use
torsion general. I haven't been able to find documentation for this.
Thanks in advance.
Hi Cathy,
Thanks for pointing out the lack of documentation on this. I'll make a note to
add some.
You need to
Sebastiano Pasqualato wrote:
Hi Paul, hi all.
I was wondering if there's a way to avoid that a new symmetry
controller window opens every time I click on the symmetry by
molecule... button of the Show symmetry? dialog, rather than just
bringing to the front an already opened one.
There
Sebastiano Pasqualato wrote:
Hi Todd,
I've also experienced the same problem with the Save coordinates
dialog window. I agree with you this is pretty frustrating.
Me too!
It is an Apple bug - it came along with 2.3.x, I think.
Paul.
Yes (indeed), the CG of a LEU is not a chiral centre - and thus is not
refined/optimised. If the the CDx atoms are misassigned, then that is
what we call a nomenclature error (I think I got the terminology from
Refmac).
The last chi angle of residues types TYR, PHE, ASP and GLU used to be
Dear Dirk, David,
2009/3/11 Dirk Kostrewa kostr...@lmb.uni-muenchen.de:
Dear Paul,
this is a feature request: I would like to attach notes to the
structure, like water or sodium, alternative conformation?,
peptide flipped, that should be displayed in the next session
like labels as a
Sangeetha Vedula wrote:
I get the dirty mmcif message in the terminal window.
This is the message I get:
dirty mmCIF file? /Users/.../r-pento.cif
Bad CIFRC_Ok on ReadMMCIFFile
init_refmac_mon_lib /Users/.../r-pento.cif had no bond restraints
For the record,
It turns out that
Frank von Delft wrote:
I dont know which version of Coot you use, but usually you can move the
separator between the maps and molecules up and down (indicated by a few
dots under the map bottom scroll bar). In this way you can make the
space you want.
Well, I second the request: it could
hari jayaram wrote:
Hello ,
I just noticed that rigid body fit zone in revision 1950 stops expecting
user mouse clicks after clicking on the first atom .
Is anyone else seeing this.
Hi Hari,
Do you mean rigid body fit or Rotate/Translate mode? (Rotate/Translate
can go into single
hari jayaram wrote:
Hi paul,
Kevin did write to me asking if I could submit a detailed bug report.
Strangely, I could not reproduce the problem. I am still running
revision 1950 ..On that day myself and one other person ( I think it was
Dr Eleanor Dodson) reported that the rigid body fit
Simon Kolstoe wrote:
Dear Cootbb,
As I am a crystallographer and not a programmer, could anyone suggest a
bash script that will go through my hard drive deleting all the pesky
coot-backup directories with their horribly long file names that
zipping software cannot cope with? Also, in a
Victor Alves wrote:
Dear all
I installed Coot with Python and GTK2 in Ubuntu Intrepid 8.10.
Ubuntu 8.10 has Python 2.5.
Since 'ccp4-others.setup' file points to Coot's directory when I check
'which python' I get version 2.6 (the one Coot provides).
Is there a way to isolate Coot's python
Kay Diederichs wrote:
Victor Alves schrieb:
One other question. In this link,
http://www.ysbl.york.ac.uk/~emsley/coot/build-info
Should I not use any builds which are red?
What about the size of the green bar?
from quick inspection I would guess that green bars mean built less
than 24
Andrii Ishchenko wrote:
You can do this using coot. Just switch on showing symmetry mates(menu
Draw-CellSymmetry). Then save the needed by Save Symmetry Coordinates
Option in menu File. Waters coordinates will be saved as well.
[changing bbs]
And just for the record, the function that David
Justin Lecher wrote:
Hi all,
what is the difference between the monomers db which is provided by coot and
the one which is provided by
refmac/ccp4? Can one interchange them?
Coot uses the Refmac dictionary. As far as I know, there should be no
differences. Yes, they are interchangeable.
Pierre Aller wrote:
On Apr 7, 2009, at 2:37 PM, William G. Scott wrote:
Looks like you might be mutating into RNA (hence the non-canonical
little r). But that is ok. RNA is inherently more interesting.
On Apr 7, 2009, at 10:48 AM, Pierre Aller wrote:
Hi all,
I am using the last version
Dear Oliver,
Antony Oliver wrote:
Dear Paul + friends,
Would it be possible to place in the (top right?) corner of the main screen (or elsewhere)
an indicator telling the user what type of restraints are currently being used for real-
space refinement/fitting? I frequently forget that I have
Antony Oliver wrote:
Paul Emsley wrote:
Dear Oliver,
Antony Oliver wrote:
Dear Paul + friends,
Would it be possible to place in the (top right?) corner of the main
screen (or elsewhere) an indicator telling the user what type of
restraints are currently being used for real-
space
Steffen Schmidt wrote:
Hi,
I experienced a weird error (amino acids are not connected) when
setting the environmental variable LANG to de_DE.UTF-8 (on a OS X 10.5
machine). I guess this language setting is screwing up the PDB file
parsing since german uses ',' as decimal separator…
William G. Scott wrote:
Could you (or we) set
LANG=en_US.US-ASCII
in the coot wrapper script?
or unset LANG
I am more than a little surprised that such a thing is not there already.
I'll add it now.
Paul.
Leonid Cherney wrote:
I tried today the new version (-0.6) and see some problems.
1. Simple mutate for nucleotides. The program makes Gr, Cr etc. in DNA
(should be Gd, Cd etc). And it does not mutate to thymine at all,
because there is no Tr. Where can I say that it's a DNA?
This has been
CK wrote:
I think perhaps I should clarify what I've been doing. I've been
refining my structure using phenix.refine and had reached a fairly
satisfactory point with suitably low R-factors (21/25) and very
reasonable RMSDs for bonds and angles. At this point I ran my structure
through the
Dear Eleanor,
Eleanor Dodson wrote:
1) The check on GLN and ASN and HIS? for likely hydrogen bonding is very
useful. Do you think it would be worth extending this to THR?
HIS is not part of the ASN/GLN check. And indeed the ASN/GLN check
works by B-factor analysis, not hydrogen bonding.
From: Christian Roth christian.r...@bbz.uni-leipzig.de
Hi all,
I am not sure but If I remember correctly Bernhard mentioned on the
last CCP4
study weekend in Nottingham that Coot is able to merge the
different water
chains, generated through repeated refinement runs, in one. If this
Maia Cherney wrote:
The general torsion function is not as good as the torsion in old X-fit.
Are you or have you ever been a member of the von Delft Pressure Group?
In x-fit you click on two atoms of a single bond and you can rotate the
rest of the molecule around that bond. This bond can
hari jayaram wrote:
Hi ..I tried a coot subversion (revision 1994) built-it-simple python on
the newest ubuntu 9.04
The build crashes just after it builds guile and ( 16-coot.txt in the
build directory ) reads :
checking for Clipper... yes
Congratulations, you are using Guile
checking for
Ed Pozharski wrote:
After recent upgrade to Ubuntu 9.04, coot binaries that worked fine
before started reporting the ELFCLASS64 error when loading a
particular library, namely /usr/lib/libguile-srfi-srfi-1-v-3.so.3.
I understand that the real root of this problem is my bizarre obsession
with
Dear Maia,
Maia Cherney wrote:
I would like to use only one-button keys, so that I could use only
one hand when fitting.
Why!? Because the other one is needed to prop up your head, maybe? :-)
http://linuxoutlaws.com/files/dan-jaunty-party-thumb.jpg
I find using my left hand for
Alex Luso wrote:
Hi Bernhard,
Thanks for the clarification.
commenting on this. Maybe there should be some low level implementation
without the use of fancy (scheme) widgets, so that at least scripts can
be run.. (on my - long - list now).
Ok, I think that would be a good idea. Given
Moritz Metlitzky wrote:
Hi everybody, i just installed coot and played around a bit with my
structure and the Fit Protein command. Now to my question, i have a zinc
atom in my structure coordinated by 3 cysteines. it refines pretty well, but
when i do Fit Protein Coot always links the 3 cys
hari jayaram wrote:
Hello Paul and everyone,
Since I had complained about difficulties in building coot from
subersion on Ubuntu Jaunty , I thought I should write in to say that I
tried building the subversion revision 2021 on ubuntu 9.04 from scratch
and it builds just fine and everything
Sebastiano Pasqualato wrote:
Hi Paul, hi all.
I have noticed that coot can't deal with spacegroup information of cns
files.
I have to substitute this:
CRYST1 87.188 49.276 132.627 90.00 108.88 90.00 P 21
with this:
CRYST1 87.188 49.276 132.627 90.00 108.88 90.00 P 1 21 1
to have
Hi Jennifer,
Doebbler wrote:
I am running Coot 0.5.2 on an intel Mac 10.5.6. I am trying to
visualize the symmetry related molecules for a small inorganic molecule
in spacegroup P 21/C. If I load the file into swiss PDB viewer or
Mercury, the symmetry operators show that I have 4
For the record/archive I'd like to conclude this thread.
It recognizes the spacegroup as P 1 21/c 1.
Is seems that Coot indeed does display symmetry correctly for this
spacegroup, but not in the way that other programs (e.g. Mercury or
Swiss PDB Viewer) do.
coot (show-spacegroup 0)
P
Oliv Eidam wrote:
Hi,
I have the same problem like Robert.
And although I updated to coot-0.6-pre-1-1941-intel-10.4-10.5.tgz like Bill
suggested, the problem (displaying no or wrong bonds) persists.
Has this problem been resolved by now? I am using OSX 10.4.11.
And
source /sw/bin/init.sh
Dear Bleeding-edge binary [1] Coot users,
I would appreciate feedback on the representation of LINKs using the
output of Buster and Phenix.refine.
(The last time I saw this in action (I don't have such files myself)
(and prior to the most recent fixes) it crashed.)
Thanks,
Paul.
[1] rev
Edward Miller wrote:
Hey Folks,
I'm working on refining a full capsid containing 60 chains.
Using the chain ID column, I've numbered my chains A-Z, a-z, and 0-7.
I was successfully able to refine my capsid in refmac using this chain
ID naming scheme.
However, coot fails to read in any of
Kevin Cowtan wrote:
Coot reads files with duplicate atom numbers
just fine (at least 0.6pre-latest does).
However Coot will ignore any lines beginning
ATOM 1?
ATOM 2?
etc
because those are not valid atom records. So that is the reason these
are being ignored.
Yes, we should say
http://thedailywtf.com/
2009-06-11
(I never get to see that dialog, of course :)
(Somehow they've got the mac version of this - apparently they don't fink
update-all often enough...)
Paul.
Valerie Biou wrote:
I run Coot version 0.6-pre-1 on a Macbook Pro. I used the fink
installation.
It crashes when I ask it to display a sequence
** (coot-real:764): WARNING **: Widget not found: sequence_view_dialog
/sw/bin/coot: line 5: 764 Bus error /sw/bin/coot-real $@
I
Simon Kolstoe wrote:
Dear cootbb,
When building into density I use a map generated from the FWT amplitudes
column and PHWT phases columns which I think is my 2Fo-Fc, and a second
map generated from DELFWT and PHDELWT which I think is my Fo-Fc.
Me too (more or less).
This
keeps me happy
Maia Cherney wrote:
If I use a *map_coeffs.mtz file from the phenix.refine, how can I turn
off the negative density?
??? Confusing question. By unclicking the is difference map? button
(you can't do this in auto-read mode, of course).
Paul.
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
William Scott wrote:
Hi Paul:
On ppc but not intel, I get this for some of the window displays (eg
density fit analysis):
Yes, we (in Oxford) have seen this before on ppc too.
We didn't resolve it. I was thinking that it was somehow picking up the
wrong fixed font. I tried adding a
William Scott wrote:
I guess I'd better brew something newer up...
All the 0.6 are pre-releases ...
Yes, indeed (I finger fumbled and posted before I added the sentence to
that effect).
Paul.
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