On 29/11/10 16:17, Nathaniel C. Gilbert wrote:
I have arachidonic acid soaked into my crystal structure and want to model it.
The phenix.refine is allowing my cis double bonds to distort to a gauche or
trans form. Is it the cif file or the refinement restraints in the program that
I need to
Credit where it's due, Coot's Get Monomer is just a wrapper for LIBCHECK.
If you look at the restraints for DTT after Get Monomer, you will notice
that chiral centres are both marked as both. Using the restraints
editor (or otherwise) change them to positive (C2) and negative (C3)
and
On 28/10/10 20:12, Changyi Xue wrote:
Hi, all
I am trying to build an oligomer ligand. I have obtained all the
cif files for the monomers from HIC-UP. I tried to build several
monomers in using coot. Then I modified the pdb file and stated the
link in the pdb head (LINKR X ABC 1 Y
On 01/10/10 16:57, Sickmier, Allen wrote:
I recently got the 24 inch Zalman and when the coot window is
maximized the 3D is reversed. I know I can minimize it slightly and
move it up and down a pixel to fix it. Has anyone found a trick to
leave it maximized and correct the 3D. I have
On 13/09/10 14:30, Oganesyan, Vaheh wrote:
I have coordinates of “small” molecule in pdf format, i.e. its an
image of pdb file and it doesn’t let me select text. The molecule has
150 atoms, so doing it by hand is not an option. How would one go
around it?
The molecule is polymyxin B and
On 03/09/10 12:44, Rex Palmer wrote:
This is not really protein crystallography but we are trying to model
build a ligand into a protein binding site. A similar ligand is
already in place and we want to replace this by initially
superimposing a phenyl ring which is common to both ligands. We
On 25/08/10 23:24, Garib Murshudov wrote:
However 1) coot uses 2mFo-DFc maps
Typically yes, but it uses whatever Refmac (or other programs) provide
(of course)
2) you should be able to feed any map you want to coot
Yes.
so it is nice place for experimenting this kind
of calculation
On 17/08/10 22:58, Rex Palmer wrote:
In Refmac: Does anyone know if lactose should be designated as one
component (Lat) or two components (Gal and Glc)?
With Refmac, you can do it both ways.
[Agree with Roger re: cif libs]
If I may add a Coot tip, I'd recommend
Extensions - Modelling - Add Other Solvent Molecules
which make such operations somewhat more slick.
Paul.
On 02/08/10 16:13, Roger Rowlett wrote:
Rex,
Glycerol should be a Refmac-recognized ligand. If you use the
On 14/07/10 12:56, Vandana Kukshal wrote:
how to make covalent bond between ligand and protein residue by using
CCp4 package
JLigand
http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html
p.s. Don't Reply if you are not following the same thread - doing so
causes confusion to threaded
On 23/06/10 14:40, Fatima wrote:
Dear all,
I'm finishing a refinement using SHELX and Coot (1.3A) and I have a modified
Arginine. There’s a blob of positive density (9.04 and 7.01 sigma) binding NH2
in the 2 conformations. I think it could be a hydroxyl there.
1) How can I add that in Coot?
Briefly (and top-postingly),
Coot does not draw covalent bonds between non-tandem residues.
Coot will represent LINK records if they are in the PDB file.
Coot will respect the links generated by JLigand if you try to do sphere
refinement.
The Coot -- JLigand internface will improve in the
Tim Gruene wrote:
I would like to use Rotate/Translate Zone in coot for a single residue and
set the
centre of rotation at the nitrogen of the subsequent residue. Is there a way to
achieve this with Coot Version 0.6.1?
No [1].
Paul.
[1] Practically no, but actually, it might be. However
Christian Engel wrote:
Dear All,
I am looking for a ccp4 program that reads in cif-files and converts
them into pdb-files, including the CRYST1 card. Can anybody suggest a
solution? I didn't find any in ccp4i, e.g. the coordinate utilities.
I also tried COOT to read in cif-files
Vinson LIANG wrote:
Dear all,
I have fit my ligand into its density with coot. Then, I add the
ligand into the protein's pdb and try to do refine with refmac5.
First, the error comes,
error message
Refmac_5.5.0109: New ligand has been encountered. Stopping now
Larry Grant wrote:
I am attempting to fit NAD to a 2.1 A lactate dehydrogenase structure
I've built and I'm running into several problems:
1. I loaded NAD from the COOT monomer library and was able to fit
roughly 2/3 of it into the density using the real space refine zone
function but the
Garib Murshudov wrote:
As I see there is no chirality definition for NAG-ASN link (perhaps
there should be but then people will be unhappy even more).
Only reason i can see for this flattening is conflict between geometry
and electron density. Your example shows that even if electron density
tirumal wrote:
Hi All,
My question is concerning geometry of NAGs in a glycoprotein structure.
Fire away...
I recently solved the structure of a glycoprotein to 3 Å and modeled
NAGs linked to Asn at 3 different places. NAGs and Asn-NAG links are
refined in Phenix.refine as per the
Did I see a PyMol screenshot (or something very like it) at the
beginning of Avatar?
James Stroud wrote:
Mike Carson claims that the spinning DNA in the computer monitor in
Jurassic Park was the product of the Ribbons software package:
http://www.cbse.uab.edu/carson/
Eleanor Dodson wrote:
In this lab there are as many takes on this as there are
crystallographers I think! It seems to depend on personality - are you a
wild optimist who traces connectivity at 0.5 Sigma - or a cautious soul
who hates to be wrong..
Blimey, I think it's the other way round.
Hussain Bhukyagps wrote:
i'm trying to solve the structure of protein with ligand.
Can any one help me in uploading ligand library (to fit in the
density) in WinCoot.
This is a good starting point:
http://www.majorgroove.org/questions/49/how-to-add-a-ligand-to-a-model
(Coot depends on
lei feng wrote:
I am wondering how to make covalent bond in coot, between a modified
substrate and regular protien residue
I can not figure out how to make the bond.
That is, perhaps, because making a bond is not up to Coot - it's a
dictionary thing.
Have a look here:
Yuan Cheng wrote:
I am trying to model a S-adenosylmethionine (SAM) molecule into the
active site of a protein using the SAH (exists in the crystal structure)
as the template.
2)Coot: I tried to superpose SAM to SAH in coot. Bot SSM superpose and
LSQ superpose didn't work. when I did SSM
hari jayaram wrote:
Hi I just started having segmentation faults with the coot downloaded
from the ccp4 releases page for ccp4-6.1.3.
This release was working quite well, and I even convinced a few
people to stop fink-ing and just download the coot dmg from ccp4.
The problem started after
james09 pruza wrote:
Dear all,
I just wonder, How to save the LSQ output in coot.
It is not clear what you mean by output.
The transformed coordinates can be saved with File - Save Coordinates...
The rotation matrix in both orthogonal and fractional form is written to
the terminal.
Paul.
amit sharma wrote:
Apologies for a non-CCP4question.
Aggh! Stop! Stop it! Stop apologising for using CCP4BB in the way
it is supposed to be used!
And not only that, this is not a non-CCP4 question.
I have a structure of a dimeric molecule, where the interfaces between
monomers is
Ethan Merritt wrote:
On Thursday 18 February 2010 14:48:57 Paul Emsley wrote:
Ursula Schulze-Gahmen wrote:
I am a new user of Coot and I haven't found an easy way of displaying the
phi/psi angle of a specific residue while I am rebuilding. I found of course
the Ramachandran plot, but i
The current remit of CCP4BB is protein crystallography. As such,
contributions from Phenix developers are welcome. Having said that, if
the question is about how to perform some operation(s) with CCP4 then
they perhaps ought to be somewhat circumspect in their response. If
after a week or so
Ursula Schulze-Gahmen wrote:
I am a new user of Coot and I haven't found an easy way of displaying the
phi/psi angle of a specific residue while I am rebuilding. I found of course
the Ramachandran plot, but i would like a way to display the main chain
geometry of a specific residue.
You
Ursula Schulze-Gahmen wrote:
I am a new user of Coot and I ran into problems with the regularize option
that I cannot figure out. My model consists of 4 fragments that came out of
Resolve. I noticed that the 5 C-terminal residues should actually be
connected between 2 fragments in the middle of
Katja Schleider wrote:
Hi everybody,
I have a question concerning a sequence alignment with the sequences
of my 4 molecules in the AU. Unfortunately I found out that the
sequences of the 4 monomers do not match exactly. I used the program
moleman and it showed me the different numbers of
rui wrote:
Hi, Dear All,
I have a mac 10.4 with 4GB memory, I thought it should be pretty fast.
However when I run coot, it's kind of slow. Even when I push the
space key to go to next residue, I can feel it is really walking to
the next residue. Is this normal or something maybe not set up
Rana Refaey wrote:
Hi all,
I am trying to use the transform map command in coot but i am getting the
following error
6:19: In expression (0.9956 -0.08709 -0.03537 ...)::6:19: Wrong type to
apply: 0.9956
the command that i used was:
(transform-map 13 (0.9956 -0.08709 -0.03537 -0.08702 -0.9962
Regina Kettering wrote:
I am running Coot prerelease dated Feb 2009 on a macbook, OS 10.6 (snow
leopard). Prior to installing Reduce and Probe I had no problems, but I have
been getting segmentation faults whenever I try to download a pdb and map from
the EDS. Errors look something like:
aidong wrote:
Although he made pymol a commercial software against
scientific spirit [snip]...
I'm sorry, but that is so breathtakingly inaccurate that I have to
respond. If we can equate freedom to extend published ideas with
scientific spirit then Warren was a pioneer of the
Sylvia Fanucchi wrote:
Hi and Happy New Year to you all
Hello Sylvia.
I have a little question about editing phi and psi angles in coot. When
I click on the residue to adjust, it brings up a Ramachandran plot with
a single dot corresponding to the phi and psi angles of the residue
JXQI wrote:
Dear All:
Sorry for this off-topic subject.
It's not off topic. CCP4BB is for protein crystallography. Discussions
of crystallographic programs are particularly ON TOPIC! But so are
media, viruses, vectors and buffers...
Having said that, you might like to consider the Coot
If I can chip into this somewhat sacrilegiously-named thread
1) I *would* use real-space refinement :), specifically Sphere
Refinement. You can dial down the
density weight if needed, of course.
2) the documentation on refining carbohydrates in Coot has recently been
updated
Francois Berenger wrote:
When I run coot in order to read the experimental MTZ corresponding
to the PDB I am viewing, [snip]
I am afraid coot is refining my molecule instead of just displaying the
map.
Well, Refmac is - at Coot's request.
This usually happens because Coot doesn't
Francois Berenger wrote:
Paul Emsley wrote:
Francois Berenger wrote:
When I run coot in order to read the experimental MTZ corresponding
to the PDB I am viewing, [snip]
I am afraid coot is refining my molecule instead of just displaying
the map.
Well, Refmac
lei feng wrote:
I am wondering , do we need uninstall the previous version of coot to
install this?
No. Many group use more than one version of Coot.
Ah, but perhaps you mean WinCoot? My (limited) experience is that you
can install right over the top of the old one.
Paul.
Tanner, John J. wrote:
Some of you might be curious about the Ajees et al debacle that Jacob
mentioned in his message. Here are two links:
Nature Brief Communication that questioned the validity of one of Murthy's
structures:
kai...@caltech.edu wrote:
first cudos to PaulKevin for the incredible speed that coot gets more and
more useable as an allround building tool -thanks!
Appreciated.
I've had a 'problem' several times now with coot and proteins containing metal clusters. Is there a way to make the real
We are please to announce the release of Coot-0.6 (including WinCoot)
Source here:
http://www.biop.ox.ac.uk/coot/software/source/releases/coot-0.6.tar.gz
Binaries from here:
http://www.biop.ox.ac.uk/coot/software/binaries/releases/
Paul.
p.s. Sorry for the cross-posting, but it is apparent
Vandana Kukshal wrote:
i want to link AMP covalently with lysine in my structure
(phosphoamide bond)how i will do this in coot and refmac .
in turbo there is option make bond but in this no option is there .
The issue here is there there is no dictionary definition of the bond
between
Jason Porta wrote:
I am currently refining a 3 ang structure and would like to do rigid body
refinement treating each residue as a separate rigid body.
Here's how you'd do it in Coot, but I'd be surprised if this was better
that the Fit Protein function already built in (you'll need
I should add that I have only seen Joel Bard's Zalman monitor briefly.
We tweaked the settings a bit to improve the representation in the
following way:
1) use nvidia-settings to override application anti-aliasing - crank it
up to 16x if you have a good graphics card
2) add to ~/.coot file
lei feng wrote:
comparing with the old version ( I used CCP4 6.0.2 on my windows xp
computer and finished my Ph.D projects.), I found the new version of
coot is kind of slow in moving to the next residue of the structure by
hitting the space. Can we adjust this to make it faster?
Yes.
Thomas Cleveland wrote:
I just looked at the source code for reduce. It seems there is a
global variable that gets returned from main(), ReturnCodeGlobal,
which is set to 0 by default. However, further down in the code is
this (in the processPDBfile function):
// adjust cliques
Sampath Natarajan wrote:
I’m currently refining the structure (2.0 A) with a cofactor PLP. The
PLP density is clearly indicates lysine residue is covalently bound
with PLP cofactor. But I don’t know how to link the cofactor and
lysine residue for further refinement. Any suggestions on how
A Leslie wrote:
BB members may be interested to know that the 2009 Nobel prize for
chemistry has been awarded to Venki Ramakrishnan, Tom Steitz and Ada
Yonath for their structural work on the bacterial ribosome.
FYI:
Scott Pegan wrote:
I am looking for a good review on SBDD that includes a few successful
attempts. Anyone know one?
Williams et al
10.1016/j.cbpa.2005.06.007
Paul.
Milya Davlieva wrote:
Dear all,
I need to make a figure which needs to consist of 2 aligned pdb files
and their electron density maps for the structures of two mutants
(with different space groups). I'm able to do this when there are two
structures that have the same space group. Could, you,
AntonioLeung wrote:
I am a novice working on protein structure. When I pick water using
COOT, too many waters picked, filling in the whole cell.
Too many - hmm. Did you, by any chance, peak-search a difference map
without first changing the default sigma cut-off to (say) 3.5?
Paul.
Huiying Li wrote:
I used Coot:findwaters facility in REFMAC (CCP4 6.1.1) to add waters
to the refined structure. Often for the well ordered water sites the
routine added two water molecules in single water site, with their
distance (~1 Angs) way shorter than allowed hydrogen bonding distance.
Ed Pozharski wrote:
So to answer your question,
there is no decent way of fixing this without compiling coot.
I agree.
What worked for me (eventually) was to build coot using autobuilder
scripts. This is not without caveat, since guile-1.8.5 fails to compile
on Jaunty. I don't know if
peter hudson wrote:
Hello all
I superposed the two different chain, which are two different subunits
of the same structure which are different in conformation with two
differen t programmes.
1) First is with O, with LSQ command, it gives the RMSD values for
different chain is 1.5A for 108
Thomas J Magliery PhD wrote:
Is there some way to fix this without compiling Coot or re-installing
with 32-bit Ubuntu?
Instructions I found by googling for Ubuntu Coot 64 bit
James Murphy wrote:
I need to model in tetrachloroaurate molecules into a structure, from
our heavy atom soak of Potassium tetrachloroaurate.
I created a pdb file by using chemdraw and exporting as an *.sdf and
opening in pymol and saving as a *.pdb (attached)
The method you used to
Zhong Ren wrote:
*** For details on how to be removed from this list visit the ***
***CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html***
Hi,
I found the message below asking whether RESOLUTION keyword is
affecting atmmap, but I found no answer. I copy that message
in 2004 to
Paul Emsley wrote:
GRID r*a*3 r *b*4 r*c*3
r=resolution(in Angstroms)
Ooops - I mean:
GRID a*3/r b*3/r c*3/r
(plus rounding up of course)
Paul.
Sascha M. Marek wrote:
Dear crystallographers!
My basic question is, how can electron density maps be moved along with
the
respective PDB coordinates?
If you have Coot, you can try Extensions - Maps - Transform map by LSQ
model fit.
Jason Porta jpo...@unmc.edu 05/09/09 3:19 PM
Hi everybody,
Sorry if this message was already asked (I could not find it in the
archives). I am making a figure of a recently solved protein structure
including the electron density. I would like the electron density to
cover only the
Partha Chakrabarti wrote:
Hi,
Could someone point me to the best ways of building a non standard ligand?
I had PEG-400 in the cryo, and the density is about twice as long as
the PEG
that is in the monomer library.
I can get the cif file for PEG-400 from prodrg (1PE). Just wondering
what is
Just a cautionary note: It might be that (for historical crufty reasons)
Coot will try to bite you if you try to read a CNS map with a .msk
extension - giving it .msk.map should be fine.
Paul.
Kevin Cowtan wrote:
Coot will read CNS maps. Is the CNS mask format different to the CNS map
format?
Hi Bernhard,
In coot, the chiral volume is computed from the ideal bond lengths and
angles using the unit cell trick already pointed out by George. (That's
because Ralf explained to me how to do it at a phenix code camp).
the esd is not defined in the monomer library. In coot, it is define
David Cobessi wrote:
Liew Chong Wai wrote:
Hi,
Good day
I am currently building my structure by using COOT. My protein is a
tetramer protein and I have fit my protein sequence into one of the
monomer of the homologous model. May I know how can I replace other
monomer with the amended
Buz Barstow wrote:
Dear All,
I'd like to add substitute a natural base (adenine) for a non-natural
base (2-aminopurine), in a molecular model of an RNA molecule.
I'd like to do this with CCP4 and Coot. Could I ask for some help please?
The CCP4 way would be to use sketcher and search for
Eleanor Dodson wrote:
Even for NAD I think I would make my own new dictionary.
I must say that I would not (in the general case that is, there may be
an argument for doing so for NAD). There will be a price to pay at
deposition time.
To address your particular problem (and Ignoring the
Paul Emsley wrote:
And for those who like the command line to convert .res to .pdb (and
have Coot):
[see attached]
Oh curses - sorry. Not everyone develops coot.
s?\./coot-real?coot?
Paul.
Partha Chakrabarti wrote:
Hi,
I am running a 64 bit Fedora 10 machine and having problems with coot,
if i say
ldd coot-real
linux-gate.so.1 = (0x5000)
libguilegtk-2.0.so.0 = not found
libgthread-2.0.so.0 = /lib/libgthread-2.0.so.0 (0x00df8000)
librt.so.1 = /lib/librt.so.1
Jayashankar wrote:
Dear Folks,
Dear gmail-user,
The last novel proteins fold were from the yr 2007(pdb statistics),
From 2007 to till date no novel fold has been identified, this mean
the present 1283 fold are the final or
should I wait, if so , with what criteria do I expect for a new
riya doreen wrote:
I have two ligands in my structure that I need to keep at a specific
distance from each other. How can I specify this restraint in refmac ?
LINK
http://www.ysbl.york.ac.uk/~garib/refmac/docs/files/coordinates.html#pdb_link
Eleanor Dodson wrote:
... Many of these are unlikely, and you may well correct them when
rebuilding.
However the pdb file output by COOT will retain the CISPEP records..
You need to check and edit these yourself..
For the record, I believe that this is no longer the case. Coot will
only
Roger Rowlett wrote:
I will second noting the loss of arp_waters in CCP4 6.1. I know there
is a find waters option in Coot 0.5.2 under Calculate...Other
modeling tools, and perhaps this is adequate, but it doesn't seem to
have as many options for fine-tuning as arp_waters did. Coot allows
for
Albert Guskov wrote:
Dear all,
I've installed coot with fink, everything works fine, except the fact
I can not solve results of my work (that makes it totally senseless
;-))
The error I get is Gtk-WARNING **: Unable to find default local
directory monitor type
Could someone point me out what is
Ethan Lai wrote:
Dear all,
I have recently installed Coot version 0.5 on Fedora 9. However, when I
tried to open a mtz file, the following error occurs.
CCP4 library signal library_file:Bad mode (Error)
raised in ccp4_file_readchar
Any advices? Thanks!
Something of a shot in
Klaus Futterer wrote:
Does anyone know how to prevent Coot from establishing a disulfide
bond between two adjacent Cys residues?
I have reason to suspect that the bond is (at least partially) reduced.
It is not possible directly to stop Coot drawing the bond given your
atoms. However, you
Winter, G (Graeme) wrote:
I have an OS X leopard machine which I would really like to get coot
working on, but it appears to involve messing with the X system and / or
fink, neither of which I really fancy. Now I appreciate that there is
something broken about the X window (no idea what
Ronaldo Alves Pinto Nagem wrote:
Dear CCP4 users,
I was using MAPPROT from CCP4 package to rotate/translate an electron
density map in order to superpose maps from different space group
crystals. However, when applying the same operations (euler angles +
translation OR rotation + translation
Partha Chakrabarti wrote:
While building from scratch in Coot (3A resolution), if I can supply
NCS operators in CCP4 format, is it possible to display NCS related
molecules in the same way as crystallographic symmetry related ones?
External scheme script is fine if that is the way..
Yes.
If
P K wrote:
I am new to the filed of crystallography. I am having trouble figuring
out what exactly does sigma level of electron density map mean.
When sigma level of a map is increased (say from 1.5 sigma to 2 sigma)
why the map covering individual residues becomes less wide and more
Dear Roberto,
Roberto Steiner wrote:
Dear all,
a problem possibly at the coot/mmdb interface...
Indeed.
If one uploads a pdb file (from phenix.refine in the example below)
that contains Hs into Coot and then writes it out (with or without any
modification done on it) Coot shifts the HG2n
john kryst wrote:
Hi all !!
Sorry for the off topic question.
It's not off-topic.
Has anyone tried installing CCP4 and coot in Ubuntu Heran Hardy 64
bit... I have been googling and tried the suggestions of Bill
Martyn's page... but no success with the amd 64 bit machine.. all the
Dear CCP4bb,
(Not really for me to announce, but here you go...)
Just to let you know (in case you missed it) that Molprobity server[1]
is serving up ToDo lists that are compatible with WinCoot.
Thanks to Bernhard Lohkamp and the Molprobity team.
[1] http://molprobity.biochem.duke.edu/
Vellieux Frederic wrote:
No, I don't have a residue 8... Since Add Terminal Residue is the only
option to extend the chain (and we see density for the missing residues)
we are at loss there
So, you *do* have a residue 9 and 10 and want to add a residue 8. Did
I understand correctly? If
Dear Nic(holas),
Nicholas Keep wrote:
I have a structure with an unsaturated lipid in the active site, which
according to the chemists has one cis and one trans double bond. I
would expect these to be controlled by the torsion angles in the cif
files.
Yes, and a planar restraint (which is
Christina Bourne wrote:
Sorry to post a COOT question on CCP4, but the COOT page seems to be
down at the moment(and I haven't yet signed up for COOTbb)
I want to fit my ligand into density by moving it around rotatable
bonds. I obtained the pdb file with Sketcher and have run it
In message [EMAIL PROTECTED] Yanming Zhang
[EMAIL PROTECTED] writes:
Hi, all,
If I have a large molecule, say 2000 aa, the coot ramachandran plot will
be lots of outliers. Now I want to do things one step at a time, i.e
checking the outliers by residue ranges such as, 1--500, 501--1000, so
Sickmier, Allen wrote:
Hi All,
Is there a way to draw surfaces in coot, or is there a nice associated
program that will draw surfaces in coot.
I know about the dotted surface but I was looking for more of a
continuous surface. Like insight or pymol.
Hi Allen,
Yes there is a way (if
Jayashankar wrote:
Dear ccp4bb and Paul emsley,
I have a problem in coot,
I could clearly see the density for some small molecule that was
present in the sample buffer. when I generate .cif from monomer sketch
library from ccp4 and use same .cif
in coot for real space refinement, the small
conancao wrote:
Dear all:
I have problem to supperimpose 2 homologous proteins(only one subunit
is homologous) in coot.Could anybody give suggestion either using coot
or other easily availabe software to superimpose homologous
structures(pdb) and give a finial superimposed pdb or picture.
Hello Byron.
byron delabarre wrote:
I'm looking for an easy way in coot to trim residues back to Cbeta.
There is now.
1) Is there an easy way to do this, other than: click mutate, click
residue, click trim to Cb, click mutate to ?
Bleugh!
2) I wrote a script but couldn't get it
Yanming Zhang wrote:
Hello,
I did the replacement soaking and it was successful. Now I want to
superimpose the two maps to show (I hate to show off but I have to) the
map diffrence of the ligand region to demonstrate that the replacement
soaking was a success. Is there a way to superimpose
Hi Brenda,
Brenda Patterson wrote:
I am doing molecular replacement with a model of sequence identity 42%.
If you used a CCP4 automated MR tool to generate your model, then the
[Post MR] Fill Partial Residues can conveniently restore side-chains
that have been Schwarzenbachered.
Have
Raji Edayathumangalam wrote:
Thanks everyone for all your suggestions.
What's the issue? Each residue has one CSV value (per residue value) and the PDB line contains many
lines of B-values per residue. This would leave us with no easy one-to-one line correlation between
the B-value column and
Dear F8 Cooters,
For the record, I'd recommend the stable release. You can even try the
Fedora-8 build:
http://www.ysbl.york.ac.uk/~emsley/software/binaries/stable/coot-0.4.1-binary-Linux-i386-fedora-8.tar.gz
Paul.
Petr Kolenko wrote:
Hi Fred,
we use this version and we did not have any
Dear Bernhard,
Bernhard Rupp wrote:
I am trying to make a few high quality shots with Coot.
There are 2 problems I am stuck with:
1) The bones do not show up when I make a screen shot from the draw
menu to raster3d
Indeed. Also symmetry atoms, atom labels, generic labels and graphics
byron delabarre wrote:
I'm having troubles with the wonderful 'unmodelled blobs' feature in
coot when I use a CNS map.
I am using the 0.4 prerelease full prebuilt for unix (running FC5).
The 0.3.3 release didn't seem to be working properly when reading in CNS
maps (crashed everytime).
James Stroud wrote:
I finked the 0.4 pre-release. It seems to work.
Good. Do use wm_ffm for a less irritating experience.
I think the binaries are broken,
I think so too. Apple broke them. AFAICS.
so don't waste your time with them.
That is more or less the advice in the Coot FAQ.
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