Re: [COOT] mutate to unnatural amino acid

Scott Horowitz wrote: I just tried using the new coot_utils.py, but now most of the extensions menu actually won't show up at all, including the replace residue menu item. If this is going to be difficult to figure out, is there a version I could go back to that might have this function intac

Re: [COOT] map level sig figs in display window

Lepore, Bryan wrote: [ coot 0.6.2-pre-1 r3064 ] in the display, when contouring a map, e/A^3 and sigma have three sigfigs, and it appears this is hardwired - is that right? sigma yes. e/A3 has, AFAICS, 5 dec pl. because i have noticed that contouring a map (e.g. 2Fo-Fc, Fo-Fc), the leve

Re: [COOT] electrostatics and screen shots

Valerie Biou wrote: hello Hello Valerie, I just updated my Coot version to 0.6.1 using Fink on Mac Intel 10.5.8 the previous version 0.6 used to output .ppm files when prompted by command screenshot/simple. those looked like the Coot screen. The new one outputs .png files, but the electros

Re: [COOT] NAD not possible to do real space refinement and rebuilding in coot

On 26/10/10 14:08, Maria Hakansson wrote: I have a rebuilding problem of a NAD molecule using coot. The NAD molecule was fetched using the load monomer command in coot and the restraints cif file was also in the library. However the program complains about "Fails to match model atom names NN7

Re: [COOT] Colour by chain

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 now, rev 3245. also is there any way of refining

Re: [COOT] display angles in radiant

On 12/11/10 10:33, Tim Gruene wrote: how can I make coot display measured angles in radiant instead of degree? Nothing you can do. (Well, other than edit the code (take out all the clipper::Util::rad2d() functions used in std::couts) and recompile :) Paul.

Re: [COOT] adding residues (feature request?)

On 03/11/10 16:12, Ed Pozharski wrote: When adding residues to the N- or C-terminus, it may be desirable that the B-factors of the new residue match that of the previous terminal residue. Right now it uses defaults (20 for main chain, 30 for side chain) which are sensible fir a well-ordered mode

Re: [COOT] NCS copy

On 25/10/10 11:19, Phil Evans wrote: Is there a way in coot to use the auto-detected NCS operator (eg from chain A to B) to transform a copy of another chain (eg chain C to D)? This arises where I have a AB dimer, and buccaneer has built additional chains C& D (different from A& B) such that

Re: [COOT] set resolution when opening .mtz's and calculating maps?

On 20/11/10 14:17, Francis E Reyes wrote: Hi all I'm wondering if there's a way to specify the low/high resolution cut off when opening/calculating a map. Presumably you mean via the conventional dialog, rather than scripting? yes. It is an "Expert Mode"option.

Re: [COOT] Problems getting Pdb & Map using EDS...

On 24/11/10 13:36, Guillermo Carrasco wrote: Oks I've solved it. It seems that the script that uses coot to built de url (coot_dir/share/coot/scheme/get-ebi.scm) don't works well. I've added this lines and now it works! <(eds-url (string-append eds-site "/sfd/")) --- (two-let

Re: [COOT] sugar refinement

On 24/11/10 00:14, jy wrote: Dear Coot and CCP4 users, I need to add a glycosylated Asn in my protein. To do it, I copied from an existing PDB file where it has 2 NAG and 1 BMA, and modeled it to the density in Coot. Then I wrote out the PDB. WHen I refined the structure again with refmac, an e

Re: [COOT] sugar refinement

On 24/11/10 14:12, Paul Emsley wrote: On 24/11/10 00:14, jy wrote: Dear Coot and CCP4 users, I need to add a glycosylated Asn in my protein. To do it, I copied from an existing PDB file where it has 2 NAG and 1 BMA, and modeled it to the density in Coot. Then I wrote out the PDB. WHen I

Re: [COOT] 1) LSQ of chain B 2) Deleted molecules still in list

On 23/11/10 10:20, Harm Otten wrote: Dear all, please help me out with a significant drawback in our coot 0.6 installation for Ubuntu 8.04+ and some Fedora boxes. 1) LSQ of chain B 2) Deleted molecules still in list We are not able to LSQ superimpose models to a B chain. The algorithm and co

Re: [COOT] Libraries for RNA

On 25/11/10 15:25, Phil Evans wrote: 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

Re: [COOT] coot startup error

On 17/11/10 21:08, Tim Fenn wrote: On Wed, 17 Nov 2010 12:30:02 -0800 Tim Fenn wrote: On Wed, 17 Nov 2010 10:30:40 -0500 Gerwald Jogl wrote: Coot works fine until you set your preferences to not show startup tips. On next start you get the following: INFO:: loading preferences file /home/j

Re: [COOT] Coot - symmetry operation label bug....

On 29/11/10 12:37, Mirek Gilski wrote: Hi All, I found a small but significant bug in Coot and WinCoot. It is giving a wrong translation for symmetry related atoms. I tested it on SO4 anion (S is on two fold axis); two symmetry related O atoms should be generated by symmetry: -y, -x, -z+1/2

Re: [COOT] Just like you can press escape on a real space refine to stop...

On 07/12/10 20:08, Francis E Reyes wrote: Can we have a dialog box pop up summarizing the geometry and asking us to accept/reject instead of reverting back? Sometimes a real space refine takes too long/gets lost when the best fit to the density is observed before that happens. Sounds like a

Re: [COOT] Coot 0.6.2 CRYST1 problems ?

On 20/12/10 14:55, David Komander wrote: Dear all I have noticed a (related?) CRYST1 problem/bug/feature. superposing 2 molecules in 2 different cells, and saving the moved molecule, changed the CRYST1 record of the saved file to the one from the reference molecule. original pdb CRYST1 60.40

Re: [COOT] Sigma levels of ncs averaged maps

When creating an NCS average map, Coot draws a box around the chain of interest and averages the map inside that. Everywhere else is set to 0. So inside the box, yes, one might expect the rms value to be a small amount larger (considering points inside the box). However, most of the ASU is s

Re: [COOT] always on mouse button mode?

On 03/01/11 22:55, Seth Harris wrote: Hi all/Paul, I spend a great deal of time stepping through stuctures residue-by-residue (space bar) and rotating the molecule to and fro as a check up. Basically I have the mouse button held down almost constantly. I wondered if it would be simple to have

Re: [COOT] how to generate density map of selected residues

On 14/01/11 13:03, jy wrote: Hi All, I tried the "mask map" function in COOT to generate density map of selected fragment. However, the map looked much better than the original 2Fo-Fc map. :-) For example, weak density now became strong density. I would find that surprising. Do compare th

Re: [COOT] bug

On 12/01/11 17:17, Ed Pozharski wrote: Bernhard, thanks for the info. Do you think that confirmation mode should be a default? I do, FWIW. I think we'll move to modern file choosers by default in 0.7 (I don't like them so much, but they are not terrible and we (I?) should move with the tim

Re: [COOT] Regularisation of residue with alternate conformation

On 27/12/10 16:48, Luca Pellegrini wrote: When I real-space refine/regularise a segment of chain, Coot ignores the residues in alternate conformation, i.e. all atom positions get updated except those of the residues in alternate conformation. How can I regularise amino acids in alternate confo

Re: [COOT] appropriate latest binary for CentOS5 32-bit

I will try to make a CentOS 4 32-bit in the next day or two. I hope that will work for CentOS 5. Paul. On 02/02/11 12:14, Sabine Schneider wrote: Hello Alejandro, You could use the excellent autobuild script and compile it yourself. http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.ph

Re: [COOT] appropriate latest binary for CentOS5 32-bit

On 02/02/11 12:03, Alejandro Buschiazzo wrote: Dear Coot-ers, sorry if this has already been asked (I really can't find that) : after some fiddling and unsuccessful exploring, I wonder what would be the correct (or best, if several Fedora-like work), latest available Coot binary, to run under Ce

Re: [COOT] coot dumps when moving around in a map in which it can't find a coordinate for.

On 14/02/11 17:21, Peter Simone wrote: I'm having a similar problem. You mean this one? Failure to find grid coordinate uvw = ( -14, 34, 21) Xmap: Internal map ASU error - P 2ac 2ab Nuvw = ( 68, 69, 75) terminate called after throwing an instance of 'clipper::Message_fatal' I'm ru

Re: [COOT] How to incorporate a self-build library into coot?

On 17/02/11 22:35, Hailiang Zhang wrote: I want to incorporate a self-build monomer (several sugars) library and want to incorporate into coot. I know REFMAC can do this by using LIBIN. For the graphic software COOT, can somebody give me any suggestions? File -> Import CIF Dictionary Refmac an

Re: [COOT] coot dumps when moving around in a map in which it can't find a coordinate for.

On 18/02/11 14:42, Andrew Purkiss-Trew wrote: On Mon, 2011-02-14 at 17:44 +, Paul Emsley wrote: On 14/02/11 17:21, Peter Simone wrote: I'm having a similar problem. You mean this one? Failure to find grid coordinate uvw = ( -14, 34, 21) Xmap: Internal map ASU error - P 2a

Re: [COOT] Fwd: exploding hydrogens during real space refinement in coot

On 23/02/11 16:04, Kendall Nettles wrote: When I real space refine my the ligand the hydrogens fly away. The ligand pdb and cif files were generated with PRODRG. I'm using Coot 0.6.2-pre1. Is this a coot problem, or with the pdb format from PRODRG? Yes - and no. Flying hydrogens occur when

Re: [COOT] save symmetry coordinates

Indeed, the feature "save all symmetry-related molecules of molecule i within X Angstroms of position P" does not exist in Coot. However, I wonder why you would want to do this. If I wanted to generate the biological assembly, then I'd use the PISA assembly interface to do that. On 23/02/1

Re: [COOT] Automatic renaming of RNA residues?

On 23/02/11 22:40, Francis E Reyes wrote: Hi all I think I may be losing my mind, but it seems that COOT is renaming my " A" 's to " Ar" upon loading the pdb.. Am I losing my mind? F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [COOT] Red Hat Enterprise Linux 6 (RHEL 6) compability issue

On 02/03/11 11:31, Robert Dagil wrote: Thanks for the quick reply. There is a libldap version on my system, in my /usr/lib folder I have a libldap-2.4.so.2. Do I need to install some other version as well. I would expect that the newer version is back-compatible - is it because Coot thinks a o

Re: [COOT] missing keyboard rotate on windows7 laptop?

On 02/03/11 12:00, Frank von Delft wrote: Hi, I have coot 0.6.1 installed on my windows7 laptop (may it fry in hell). So I tried the Q/W/E/R/T/Y keys which are meant to rotate about the X/Y/Z axes respectively. Nothing happens, except a console message saying: Key 113 not found in binding

Re: [COOT] Red Hat Enterprise Linux 6 (RHEL 6) compability issue

On 02/03/11 12:25, Robert Dagil wrote: Tried to make a ln -s libldap-2.2.so.7, now a new ELF class error is created :o( Ah, OK, remove that link then in coot's lib dir, it's pointing to the the wrong lib/directory. Try again. You need to link to the 64-bit ldap lib (which I guess is in /us

Re: [COOT] Red Hat Enterprise Linux 6 (RHEL 6) compability issue

On 02/03/11 13:38, Robert Dagil wrote: OK, so after doing ln -s on the following, pointing all to /usr/lib64 COOT starts up! Amazing libldap-2.2.so.7 -> /usr/lib64/libldap-2.4.so.2 libssl.so.4 -> /usr/lib64/libssl.so.1.0.0 libcrypto.so.4 -> /usr/lib64/libcrypto.so.1.0.0 Thanks for all y

Re: [COOT] Fwd: exploding hydrogens during real space refinement in coot

On 23/02/11 16:26, Paul Emsley wrote: On 23/02/11 16:04, Kendall Nettles wrote: When I real space refine my the ligand the hydrogens fly away. The ligand pdb and cif files were generated with PRODRG. I'm using Coot 0.6.2-pre1. Is this a coot problem, or with the pdb format from P

Re: [COOT] where to change default settings on Windows

I did manage to get coot loading a pdb file as a C-alpha trace by placing the statement graphics_to_ca_representation(0) in the .coot.py file where. I suppose 0 is the number of the molecule. So my question is can this be made permanent so that when I load another pdb file in the same coot session

Re: [COOT] coot dumps when moving around in a map in which it can't find a coordinate for.

On 18/02/11 14:42, Andrew Purkiss-Trew wrote: On Mon, 2011-02-14 at 17:44 +, Paul Emsley wrote: On 14/02/11 17:21, Peter Simone wrote: I'm having a similar problem. You mean this one? Failure to find grid coordinate uvw = ( -14, 34, 21) Xmap: Internal map ASU error - P 2a

Re: [COOT] Hydrogen woes

On 16/03/11 18:45, Dr. Mark Mayer wrote: Dear all, I'm rebuilding structure refined using phenix -1.7-650 using coot 0.6.2-pre-1-250. When I use the rotamers command to select new rotamers (flagged as bad by molprobity) some of the riding H atoms get left behind, which means the file is no good

Re: [COOT] Hydrogen woes

, Paul Emsley wrote: On 16/03/11 18:45, Dr. Mark Mayer wrote: Dear all, I'm rebuilding structure refined using phenix -1.7-650 using coot 0.6.2-pre-1-250. When I use the rotamers command to select new rotamers (flagged as bad by molprobity) some of the riding H atoms get left behind, which

Re: [COOT] Hydrogen woes

On 17/03/11 14:37, Garib N Murshudov wrote: First, Coot uses the "old-style" filenames - i.e. the .cif files [1] are in lettered subdirectories, not all files in one directory (straightforward for me to fix if you mean to keep the new naming style). They are not in one directory. The st

Re: [COOT] "select filename for saved coordinates" window hidden by main window

On 22/03/11 14:40, Sebastiano Pasqualato wrote: does everybody, like me, get the "select filename for saved coordinates" window popping up under the main window, when trying to save a pdb file? Only Mac users. Is there a way to avoid it? Don't use a Mac? :) I know, stupid idea... I

Re: [COOT] density fit scale factor

On 22/03/11 21:57, Bryan Lepore wrote: the manual has a rule of thumb for the density fit scale factor, just wanted to confirm the math: 1 / ( 4 X sigma ) where sigma is the sigma of the map. Yes, that's what the manual says - I have no reason to disbelieve it at the moment. Paul.

Re: [COOT] Hydrogen woes

I'd just like to clarify a bit (in the light of the conversation with Garib). I tested the new version and it seems to work well - for proteins at least. Download the Refmac dictionary: http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac_dictionary_v5.26.tar.gz create a

Re: [COOT] Hydrogen woes

Yes, sorry the env var was a typo. On 03/30/2011 05:44 PM, Andreas Förster wrote: Hey Paul, in revision 3315, I also had to use the variable name COOT_REFMAC_LIB_DIR to read it the new dictionary, and I get the same "problem reading link angle mmCIFLoop" warning. Ah, me too. So angle in lin

Re: [COOT] Hydrogen woes

On 30/03/11 10:44, Andreas Förster wrote: in revision 3315, I also had to use the variable name COOT_REFMAC_LIB_DIR to read it the new dictionary, and I get the same "problem reading link angle mmCIFLoop" warning. OK, I have tracked this down - it was due to the use of _chem_link_angle.linkId

Re: [COOT] NCS maps

Yes, but... you might not get what you want, because NCS maps are transformed on the fly, I believe, so if you write out an NCS map, you will get the map you first started with (IIRC) - maybe that was what to which Dave was referring. I think that if you make a map using "transform map via ls

Re: [COOT] low res real-space refinement

I agree with that. Also, tweak down the x-ray weight in the refinement to perhaps 10 or so. Additionally, and recently, there is add-extra-start-pos-restraint, but that is clumsy to set-up by hand. I will see if I can do something about that. Paul. On 14/04/11 10:32, Bernhard Lohkamp wro

Re: [COOT] low res real-space refinement

Let's be clear what you mean, do I understand correctly? You are refining one residue and you want that residue to know about it's environment - i.e. residues that have not been selected for refinement and won't move, but will influence the refinement because they can provide vdW or H-bond res

Re: [COOT] Smooth recentering in startup script

On 15/04/11 14:54, David Schuller wrote: I like to cut down the number of steps for smooth recentering due to the (lack of) speed of my graphics. How can I put this in one of the startup scripts rather than clicking through the menus every time? A slightly confusing question. You should need

Re: [COOT] problems building low resolution protein-DNA complex

On 04/20/2011 01:57 PM, david lawson (JIC) wrote: Dear All, I am building and refining a protein-DNA complex at 3 Ang resolution and having a bit of trouble with side-chains that interact with DNA. In particular Arg side-chains that H-bond to the phosphate backbone tend to get dragged into

Re: [COOT] Possible to get fractional coordinates of selected atom in the status bar?

On 20/04/11 15:48, Francis E Reyes wrote: Hi all I'm currently in the process of completing a heavy atom model so I need to be able to compare fractional coordinates of possible heavy atom's (fractional seems the easiest way to think about it for me). Is there anyway to get the heavy atom fracti

Re: [COOT] Custom Covalent Bond in Coot

On 22/04/11 05:44, Matthew Bick wrote: What I would like to know is 1) How do I tell Coot this is a real bond so it is properly displayed, It is a real bond - it is dashed because it is a LINK - LINKs descriptions not used in refinement. and 2) How can I create a dictionary with the prope

Re: [COOT] Coot window problem after patch

The warning message suggests that your "patch" broke accelerated X11. To check, $ xdpyinfo and look for GLX if it is not there your X11 can no longer make OpenGL drawing-areas/windows. That needs to be fixed obviously. Paul. On 29/04/11 14:02, Yong Y Wang wrote: The patch is called a se

Re: [COOT] Python problem

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 on the version copied across from where it worked, and also from the latest b

Re: [COOT] Python problem

On 04/05/11 13:11, Phil Evans wrote: Is that dangerous? Not really, python makes the pyc files again (I understand). If I move it I then get ImportError: Bad magic number in /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site.pyc after moving that I then get Import

Re: [COOT] accessing console output

So, no, not really. I suppose the right thing to do is for the map-reading routine to return a python object. I can do that if that would help. What sort of thing is failing? Paul. p.s. damn and blast Microsoft exchange/web-mail Grrr.. From: Maili

Re: [COOT] script to delete waters below 0.8 e/A^3

On 03/06/11 23:11, Seth Harris wrote: Hi all, I often use the Check/Delete waters dialog to delete only those waters below 0.8 level in the map. I do this often enough that it is high time to find/create a script version, preferably even something I could launch from the command line, or barr

Re: [COOT] script to delete waters below 0.8 e/A^3

On 07/06/11 22:58, Seth Harris wrote: Thanks Paul, You think of everything, if only I always knew how to find it... I added this line to my key bindings: (add-key-binding "Goodbye weak waters" "z" (lambda () (delete-checked-waters-baddies 0 300 0.8 2.0 3.8 0 0 1))) so that this works on the

Re: [COOT] script to delete waters below 0.8 e/A^3

On 08/06/11 08:00, Frank von Delft wrote: Surely using an absolute sigma cut-off is not a very sensible thing to do - given that sigma is a function of so many different things that have nothing to do with noise? If you have val in electrons/A^3, then use (/ val (map-sigma (imol-refinement-ma

Re: [COOT] How to connect two atoms?

On 14/06/11 04:15, 曾福星 wrote: > Hi all, > In my structure, a glycosylation site was been found. I have put a > GlcNAG beside the glycosylation site, ASN. Now, how do I connect the > GlcNAG to the ASN? > Coot will not draw a (conventional) bond between ASN and GlcNAG. If you want to show that they

Re: [COOT] residue or during mutate, etc.

Hi all, Hi Joanne, I am new to coot. I like it so far but I have reached a problem when attempting to refine. The residues mutated in the pdb are saved but out of order. OK, let's be clear what you mean here. Do you mean that the atoms of the residues are out of order (and the residues

Re: [COOT] changing bond length

I have to mutate 6 membered ring structure, with 2 Natoms and 4 C atoms. We are talking about modifying a ligand, I take it? There was no hydrogen atom on the nitrogens. after necessary mutations i have add a hydrogen atom on one of these N atoms. Using some tool other than Coot, I presume?

Re: [COOT] changing bond length

If we are talking about modifying restraints, then changing the bond length does not change the bond order. I am not convinced that we are talking about Coot. Using the restraints editor is the the recommended way of manipulating chemistry. Err, just for the record, I mean that the restraints

[COOT] Release 0.6.2

Dear All, We are pleased to announce the release of Coot 0.6.2. You can find the binaries here: http://lmb.bioch.ox.ac.uk/coot/software/binaries/releases/ http://www.ysbl.york.ac.uk/~emsley/software/binaries/stable/ http://www.ysbl.york.ac.uk/~lohkamp/software/binaries/stable/ For Mac builds,

Re: [COOT] Release 0.6.2

On 13/07/11 21:35, Tim Fenn wrote: On Wed, 13 Jul 2011 19:52:19 +0100 Paul Emsley wrote: Dear All, We are pleased to announce the release of Coot 0.6.2. Congratulations! Just a quick question - does 0.6.2 corresponds to SVN tag 3560? It looks like there were some commits to the 0.6.2

Re: [COOT] Release 0.6.2 for OS X (10.6, 64-bit intel)

On 13/07/11 22:06, William Scott wrote: I build what I understood to be 0.6.2 on July 7th and posted it here: http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot Ah - thanks. http://www.biop.ox.ac.uk/coot/software/source/releases/ Is this the right thing? Yes. The binary bu

[COOT]

On 13/07/11 17:56, Alexander Fedorov wrote: I am looking for COOT quick detection of waters in special positions in any PDB file. Coot doesn't do that :-( Paul.

Re: [COOT] Multiple, overlapping pointer distances

On 06/07/11 17:03, Andrew T. Torelli wrote: I commonly use 'Pointer Distances' when I have multiple, superimposed structures displayed. I find that the displayed distances often overlap each other and are therefore hard to read when measured/displayed between the pointer and atoms in

Re: [COOT] menu font size

I am not sure that that is what Sebastiano means. I think he means the font of the GUI - and if so, I agree - whenever I have had occasion to install coot from one of Bill's packages, I find that the fonts are too big (they used to be smaller and nice). It is something to do with the theme.

Re: [COOT] ubuntu coot fails on monomer search

On 15/07/11 16:05, Ed Pozharski wrote: First of all, let me say that having coot packaged for Ubuntu is fantastic. Not only it makes it easier to install, to me another important consequence is the the Linux small-size promise is thus fulfilled. I believe that Morten is using 0.7-pre for the p

Re: [COOT] missing C7 when mutating DNA

On 10/08/11 18:17, Sabine Schneider wrote: Hello, I am using COOT 0.7 pre 1 rev 3602. Very adventurous :) If I mutate a DNA nucleotide to dT (DT) the C7 (or C5M) is missing. Hmm... Coot allows you to do that? Using the simple mutate button? Oh dear. Must fix. This is happening with 'o

Re: [COOT] Feature request - automatic conversion of Nucleic acid to v3.2 format

On 18/08/11 16:36, Nat Echols wrote: On Thu, Aug 18, 2011 at 5:41 AM, Huw Jenkins > wrote: Having spent a while on the CCP4bb trying to fix what I thought was a Coot library problem but turned out to be an issue with the input pdb file, and as was sugg

Re: [COOT] Adding nucleotide to RNA chain fails with ERROR:: nucleotide_to_nucleotide() unassigned type

On 16/08/11 21:21, Kevin Keating wrote: I think I've fixed the problem for adding RNA nucleotides. One of the internal Coot functions wasn't fully updated with the new residue names (i.e A and C instead of Ar and Cr). Try out 0.7-pre-1 revision 3628 when it gets packaged for OS X and let

Re: [COOT] current Spacenavigator support

On 25/08/11 15:04, Priit Eek wrote: I wonder if anybody has actually gotten the 3DConnexion SpaceNavigator to work with Coot.. Not to my knowledge. My understanding is that we were waiting for useful support of the device at the X11 level. If that is in place, then Coot can be tweaked to

Re: [COOT] torsion restraints not working in newly installed coot 0.7-pre-1

On 25/08/11 18:20, Richard Rymer wrote: I finally upgraded to 0.7 this morning via fink, but this seems to have caused a severe problem: torsion angle restraints are no longer functioning in real space refinement. Specifically, torsion angle restraints are turned on under refinement control, b

Re: [COOT] opening .phs file output from SHELXE

On 05/09/11 12:34, Robert Cleverley wrote: No body. The recommended method is to use the fcf output of shelx. Paul.

Re: [COOT] Why can not my ligand be refined in coot?

On 08/09/11 11:12, Maria Hakansson wrote: I have a problem with a ligand made in the ccp4 program sketcher. The ligand has good geometry and a library description - dictionary, has been created called aln_mon_lib.cif together with structure as aln-libcheck.pdb. The dictionary has been read in co

Re: [COOT] Add OXT broken?

On 15/09/11 22:53, Jonathan Winger wrote: When I try to add an OXT to my model, coot crashes. Specifically, when I try to change the chain from the list in the popup window (below), it hangs then completely crashes. I'm on an intel mac running 10.6.8, with Coot 0.7-pre-1 (revision 3628). Bug

Re: [COOT] Nomenclature errors

On 15/09/11 17:47, Engin Özkan wrote: Dear coot users and developers, We are using coot 0.7-pre-1 (rev 3633) in the lab on linux and Mac machines, and have observed something odd that we did not see before. Most (all?) pdb files when opened give a (harmless) warning that says "Molecule x has nom

Re: [COOT] ligands

On 21/09/11 16:10, Mike wrote: It looks like the new Coot no longer recognizes * for the sugar atoms in ATP, UDP, etc. That's right. Has anyone else had this problem? Yes. I think the solution for now is to run molprobity's remediator. A longer-term solution is for Coot - or a ccp4 prog

[COOT] Fwd: Re: colour by sequence similarity

try again... Original Message Subject:Re: colour by sequence similarity Date: Thu, 29 Sep 2011 11:32:58 +0100 From: Paul Emsley To: COOT@JISCMAIL.AC.UK On 28/09/11 10:05, Tim Gruene wrote: is there a way in coot to colour a molecule according to the

Re: [COOT] ball-and-stick issues

On 30/09/11 19:58, Judit Debreczeni wrote: 1. Displaying ball-and-stick representation of a residue turns dashed lines representing LINKs ball-and-stick style for other (unrelated) residues. Driver bug, IMHO. 2. Ball-and-stick representations are undisplayed and can no longer be turned on usi

Re: [COOT] Reading cif files at start

On 06/10/11 08:41, AFL wrote: Dear All, I have a number of cif files generated for my structure and would like to read them in at coot start. Right now I'm doing it with an alias replacing coot with a 'coot --dictionary ...' but I feel like there must be an easier way... like automaticall

Re: [COOT] Reading cif files at start

On 06/10/11 11:24, Paul Emsley wrote: On 06/10/11 08:41, AFL wrote: Dear All, I have a number of cif files generated for my structure and would like to read them in at coot start. Right now I'm doing it with an alias replacing coot with a 'coot --dictionary ...' but I

Re: [COOT] Alternative conformation refinement issue

On 06/10/11 15:15, AFL wrote: Dear All, I have following definition of ligands in my active site: ATOM 5137 N1 APPE C 1 -40.239 -29.350 18.293 0.59 8.21 N ATOM 5138 C2 APPE C 1 -39.254 -30.307 18.165 0.59 10.70 C ATOM 5139 C2AAPPE C 1

Re: [COOT] distances not being displayed in 0.7-pre-1

On 14/10/11 17:15, Scott Classen wrote: Hello, I've installed Coot 0.7-pre-1 (revision 3632) via fink on my Mac running OS X 10.7.2 Atom labels are working correctly, but the distances are not being displayed. The dotted lines connecting two atoms are displayed, but not the text indicating the

Re: [COOT] key binding on OS X 10.7

On 24/10/11 10:00, Jianghai Zhu wrote: To follow up this problem. No user-defined keybindings work with either Paul's keybinding or Bernhard's keybindings. The standard key bindings worked fine. However, if I hit ^g (keyboard-go-to-residue), many standard keybindings didn't work anymore. I

Re: [COOT] building coot from scratch

On 28/10/11 23:33, Richard Baxter wrote: Dear All, A recent X11 package update seemed to break my Coot, so I downloaded the build_coot_from_scratch script and ran it. It downloaded lots of stuff but when I went into the coot-0.7-pre-1 subdirectory and ran "./configure", it failed with the err

Re: [COOT] Coot for OSX 10.6

On 31/10/11 09:35, William G. Scott wrote: I haven't been able to compile coot since 11 September, due to a change in the code. I've got a 10.6.8 version of that too, but nothing newer I am afraid. I think that this is a python bug. When I get back (in a few days) I will have another bash

Re: [COOT] Coot for OSX 10.6

On 31/10/11 11:22, Ben Eisenbraun wrote: On Mon, Oct 31, 2011 at 10:51:21AM -0400, Paul Emsley wrote: When I get back (in a few days) I will have another bash at compiling on Mac myself. When do we get the build-it-gtk2-darwin-x11-simple script? I imagine we'll see that before the bui

Re: [COOT] Multiple sessions of Coot on Mac

On 31/10/11 13:05, Yang, Jie wrote: Hi, I am new to Mac (OSX 10.6.8). I am wondering how to open several Coot sessions on Mac? Yes, I think so. If you don't want the output files stepping on each other, then you could start the coots in different directories. Or use the --no-guano option

Re: [COOT] display part of PDB file as bonds

On 08/11/11 10:33, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, is it possible to display only one part of a molecule (i.e. one chain) as bonds and the rest as C_alphas, without splitting the PDB file into two and loading them separately? No, sorry. Paul.

Re: [COOT] svn coot 3743 not loading map and pdb after refmac run

On 08/11/11 23:16, hari jayaram wrote: Hi, I upgraded and compiled coot from the svn branch after a few months of using an older svn commit id. The new svn 3743 coot with python (build-it-gtk-simple python) on a 64 bit Ubuntu 10.04 box does not seem to load the map and pdb after a refmac run from

Re: [COOT] Problem running 0.6.2

On 15/11/11 12:22, Paula Salgado wrote: Dear all I've been running Coot 0.6.2 for a few months after automatic installation of CCP4. I use Ubuntu 11.04. (32 bit). After an automatic update of Ubuntu, Coot stoped working with the error message: *** Cannot find the double-buffered visual. **

Re: [COOT] request to download free coot tutorial with free downloadable PDB file and mtz file used in the tutorial

I think that the manual describes baton building reasonably well. There is also Tutorial 2. For the best teaching, be sure to be at Model-Building session 2, X-ray methods, CSHL in October... (haha). (And of course, a CCP4-using crystallographer would try buccaneer first before thinking of

[COOT] Fwd: Re: Coot v0.7 on Mac OSX 10.7.2 -

Original Message Subject:Re: Coot v0.7 on Mac OSX 10.7.2 - Date: Mon, 21 Nov 2011 16:48:05 + From: Paul Emsley To: COOT@JISCMAIL.AC.UK See Section 3.4 of the FAQ. Paul.

[COOT] Fwd: Re: Check Waters _Below_ Some B-factor

Original Message Subject:Re: Check Waters _Below_ Some B-factor Date: Mon, 21 Nov 2011 16:49:02 + From: Paul Emsley To: COOT@JISCMAIL.AC.UK On 18/11/11 17:02, Jacob Keller wrote: Dear Coot list, is there a way in Coot to check for waters that are

[COOT] Fwd: Re: question related to baton backward build

Original Message Subject:Re: question related to baton backward build Date: Mon, 21 Nov 2011 16:47:29 + From: Paul Emsley To: Dialing Pretty CC: COOT@JISCMAIL.AC.UK On 19/11/11 08:13, Dialing Pretty wrote: Dear All, In Page 29 of the Coot user

[COOT] Fwd: Re: question related to peptide baton build

Original Message Subject:Re: question related to peptide baton build Date: Mon, 21 Nov 2011 16:47:43 + From: Paul Emsley To: Dialing Pretty , "COOT@JISCMAIL.AC.UK" On 19/11/11 06:39, Dialing Pretty wrote: Dear All, I am using baton to build

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