Re: [COOT] Coot Performance on Intel HD Graphics 5000

2014-03-28 Thread Paul Emsley
On 28/03/14 08:35, Kay Diederichs wrote: Am 28.03.14 08:44, schrieb Folmer Fredslund: Hi Kay, Ethan and Dale, I don't want to turn this into a me too thread, but I can confirm that I also see this issue. My system is a 64bit Ubuntu 12.04 kernel 3.11, with the HD3000 graphics on an i7-2640M

Re: [COOT] Symops in atom_info_text accessible by scripting?

2014-03-29 Thread Paul Emsley
On 28/03/14 15:27, Oliver Clarke wrote: Hi all, Is it possible to access from the scripting interface the symmetry info in the atom_info_text string displayed when a user clicks on an atom? I would like to write a little function that creates a new copy of whatever symmetry molecule the user

Re: [COOT] Symops in atom_info_text accessible by scripting?

2014-03-29 Thread Paul Emsley
On 29/03/14 19:13, Oliver Clarke wrote: Hmm, that’s a good idea, I’ll try it… I don’t think symm shift reference chain takes an atom spec though does it? It doesn’t seem to take any arguments so I assume it just takes the current cursor position - I guess I could use go to atom and

Re: [COOT] Jiggle fit scale factor meaning?

2014-03-29 Thread Paul Emsley
PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote: On 29/03/14 19:19, Oliver Clarke wrote: Hi all, I was wondering if anyone could shed some light on what the scale factor in jiggle fit represents? Empirically, I’ve found that a value of 0.1 with 1000-1 trials seems to work pretty well

Re: [COOT] Merge molecules scripting function

2014-04-03 Thread Paul Emsley
On 03/04/14 04:45, Oliver Clarke wrote: Hi all, Is the functionality of ‘Calculate--Merge Molecules’ available from the scripting interface? Yes. I couldn’t find it in the manual. There is a function named merge_molecules, but I don’t know what arguments it takes and it does not do what I

Re: [COOT] How to complete a residue?

2014-04-11 Thread Paul Emsley
Hello Renate Gessmann, On 11/04/14 04:19, Renate Gessmann wrote: How do I complete a residue when I have only one atom (for example the SG in Cys as part of a disulfite bond), but nice density without neighboring residues? So, a 'add terminal residue' is not possible, If I understood

Re: [COOT] How to complete a residue?

2014-04-11 Thread Paul Emsley
Hello Renate Gessmann, On 11/04/14 04:19, Renate Gessmann wrote: How do I complete a residue when I have only one atom (for example the SG in Cys as part of a disulfite bond), but nice density without neighboring residues? So, a 'add terminal residue' is not possible, If I understood

Re: [COOT] Removing atom labels permanently

2014-04-28 Thread Paul Emsley
This adds a key-binding (Shift+L) that removes all the current atom labels: (add-key-binding Remove labels L (lambda () (remove-all-atom-labels))) (Not for Windows, of course.) HTH, Paul On 17/04/14 08:05, Bernhard Lohkamp wrote: Hi Grant, to remove all labels (via GUI Measures-Clear atom

Re: [COOT] density fit scoring

2014-05-21 Thread Paul Emsley
On 20/05/14 15:10, George Devaniranjan wrote: Hi, Hi George, Sorry for the delay. I am new to COOT Hello. Welcome. and electron density analysis and I have been reading the manual and the tutorials so far. I have a question to which I have yet been unable to find an answer. It's

Re: [COOT] Structure factors to CCP4 maps

2014-05-27 Thread Paul Emsley
On 27/05/14 22:42, RiC wrote: HI, Does anyone have a step by step guide to go from a structure factor file from the PDB to a CCP4 map (understandable to a biologist) like the one I can download on the electron density server? Hi Patrick, Depending on the program with which you will view

Re: [COOT] truncate/modify a MTZ file

2014-05-29 Thread Paul Emsley
On 30/05/14 00:17, George Devaniranjan wrote: Thank you for your reply, Dale. Let me rephrase the question: Essentially I want to use COOT's Calculate--map sharpening OK, so you know how to do that, I presume but only use the backbone atoms in the process. So mask out the other atoms:

Re: [COOT] No graphics window on osx 10.9

2014-06-02 Thread Paul Emsley
On 02/06/14 16:15, Thomas, Leonard M. wrote: Hello All, I just upgraded my Mac to 10.9. I have tried both the stable version of coot 0.7.1 and also a daily build of 0.8 and still have the same problem of no graphics window showing up. The terminal output ends at

Re: [COOT] Map sharpening

2014-06-03 Thread Paul Emsley
the following reply by Paul Emsley: */It scales all amplitudes (whichever you chose when you read in the mtz file) by the application of a negative (or positive) B-factor. So the scale factor is a function of resolution and nothing more (at the moment)./* */Paul./* So just to clarify

Re: [COOT] coot crash when loading mtz file

2014-06-19 Thread Paul Emsley
On 18/06/14 19:09, Thomas, Leonard M. wrote: OK this has me puzzled. Coot was working fine until I had to update something in order to install the latest version of Phenix. I don't remember exactly what the module was but Phenix needed it. Now the latest version of Coot crashes when loading

Re: [COOT] coot crash when loading mtz file

2014-06-19 Thread Paul Emsley
On 19/06/14 11:29, Paul Emsley wrote: On 18/06/14 19:09, Thomas, Leonard M. wrote: OK this has me puzzled. Coot was working fine until I had to update something in order to install the latest version of Phenix. I don't remember exactly what the module was but Phenix needed it. Now

Re: [COOT] Serine modification on COOT

2014-07-22 Thread Paul Emsley
On 21/07/14 19:20, jesu...@uci.edu wrote: Hi Everyone, I am trying to model an acyl serine residue. What is the easiest way to input the modified amino acid into the structure so I can refine the structure? The modification on serine is propanoyl and butanoyl. Thank you in advance! Centre on

Re: [COOT] Coot draws bonds badly for SHELXL model

2014-08-01 Thread Paul Emsley
Hello Dale, Sorry for the delay. On 26/06/14 17:30, Dale Tronrud wrote: You will be distressed to hear that I'm back to refining my model which has broken every crystallographic program. Today seems to be Coot's day. As you see in the screen shot I have two pytol tails from Bchl-a

Re: [COOT] [ccp4bb] Help with importing density fit bar plots from Coot

2014-09-02 Thread Paul Emsley
On 02/09/14 15:06, amit sharma wrote: Hi, Density fit analysis in Coot plots the real space R-factor for each residue. Is it possible to import these values for each residue? If you are using the coot package, you can use density-score-by-residue to get these numbers as text. Paul.

Re: [COOT] Rotate-Translate fragment shows hydrogens

2014-09-04 Thread Paul Emsley
On 02/09/14 23:59, Mark A Saper wrote: Is there anyway to prevent the rotate-translate fragment from showing the hydrogens in the model? The answer, I'm sad to say, is no, not yet. It would be a good if Coot followed the current drawing mode of the main molecule for the temporary atoms (I

Re: [COOT] extensions menu is gone

2014-09-06 Thread Paul Emsley
...@crystal.harvard.edu mailto:z...@crystal.harvard.edu Cc: William G. Scott wgsc...@ucsc.edu mailto:wgsc...@ucsc.edu, Paul Emsley pems...@mrc-lmb.cam.ac.uk mailto:pems...@mrc-lmb.cam.ac.uk Subject: Re: extensions menu is gone Hi Jianghai, I think I solved the problem at the time by downgrading

[COOT] Note to Coot Compilers

2014-09-09 Thread Paul Emsley
Dear All, As of revision 5285 the coot dependencies, as thus coot code itself has undergone an overhaul. The build script builds new versions of python, mmdb, clipper and ssm and is now called build-it rather than build-it-gtk2-simple. I'd recommend scrapping the current installation

[COOT] Release 0.8

2014-09-23 Thread Paul Emsley
We are pleased to announce the release of Coot 0.8. New binaries should be on their way shortly: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/ http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/release/ o FEATURE: Added an interface for Cootilus o

Re: [COOT] COOT failed loading monomers

2014-09-23 Thread Paul Emsley
On 23/09/14 19:12, Vijaykumar Pillalamarri wrote: Dear all, I have recently installed COOT 0.7.1. When I tried to load monomers (like Glycerol), nothing is loaded onto the GUI. Do we have to link monomer library to COOT to be able to load monomers on COOT? if so, please help me to get

Re: [COOT] making difference maps in Coot -- under the hood

2014-10-02 Thread Paul Emsley
On 01/10/14 16:32, Doeke Hekstra wrote: As a novice to making electron density difference maps, I am curious about the algorithm underlying the “make a difference map” option in Coot. My impression is that the subtraction occurs in real space rather than at the level of structure factors.

Re: [COOT] Release 0.8 Re: Coot performance on Intel HD

2014-10-02 Thread Paul Emsley
On 01/10/14 13:40, Marcin Wojdyr wrote: A few days ago I've reported the issue with squares to freeglut developers and they removed the points: https://github.com/dcnieho/FreeGLUT/issues/19 For the coming ccp4 release we'll go with stroke-characters enabled by default (for Linux only) and with

Re: [COOT] COOT failed loading monomers

2014-10-07 Thread Paul Emsley
On 07/10/14 11:35, Vijaykumar Pillalamarri wrote: Dear Paul, I downloaded the binaries from coot official website only. :) I think I have to link the monomer library to coot after installation for it's proper functioning. That should not be needed... When I tried to load GOL from

Re: [COOT] change atom name

2014-10-08 Thread Paul Emsley
On 07/10/14 15:37, Schmitzberger,Florian wrote: Hi everybody, Is it possible in COOT to change the designation of an atom? Specific case, I downloaded an CSX with terminal carboxy group oxygen designated OXT. I would like to change it to a simple ‘O’. No, you can't do that. Not easily,

Re: [COOT] SMILES not responding

2014-10-08 Thread Paul Emsley
On 08/10/14 09:37, Lau Sze Yi wrote: Hi, I tried to open SMILES in COOT under Files -- SMILES but did not get any response. What is wrong? Is there any other way of getting around this problem? I am trying to build Jeffamine-ED2003, currently not available in ligand library. Hi,

Re: [COOT] couple of minor bugs/changes in behaviour

2014-10-14 Thread Paul Emsley
On 13/10/14 15:31, Oliver Clarke wrote: Just an update to the first of these issues - this only seems to be the case when I select Jones Rainbow using the change_model_molecule_representation_mode() function, which I bind to keys as below so that I can quickly cycle between representation

Re: [COOT] 2 bugs+1 question, OS X version

2014-10-18 Thread Paul Emsley
Hi Mark, Sorry for the delay. On 01/10/14 11:22, Mark A Saper wrote: I am running the standalone version of Coot 0.8-stable version on Mac OS X 10.9.4 compiled for 10.9 only. I encountered 2 errors (I can live with them, but I thought you should know). 1. Upon exiting Coot I receive these

Re: [COOT] Display problem in coot _residue fit

2014-11-04 Thread Paul Emsley
On 04/11/14 20:35, Jan Stransky wrote: Hi Dorothy, this dashed lines represent links. Yes - you can tell this because they are drawn in the same colours as the molecule with the half-bond colour scheme. You can delete them in PDB-file, look for keywords LINK and LINKER. LINK and LINKR.

Re: [COOT] protein_db.cpp build errors on linux

2014-11-14 Thread Paul Emsley
Hi ... err.. bbc :) On 14/11/14 12:52, bbc wrote: I'm trying to build latest coot source on a CentOS 6.5 machine, but I get a compilation error for coot-0.8.1-pre/protein_db.cpp, namely it looks like it complains that a class is undefined. Here is the compilation line and error output:

Re: [COOT] pdb info - where?

2014-11-18 Thread Paul Emsley
On 19/11/14 13:26, Frank von Delft wrote: Hi all - does coot have a way to let me see the pdb header? There is a remarks browser under About (Yes, I know I can open a text browser - but that's typically about 20 clicks, especially if I pulled the coordinates directly from the PDB.)

Re: [COOT] problems with validate waters

2014-11-19 Thread Paul Emsley
On 19/11/14 20:22, Tobias Beck wrote: Hi all, I am using Coot 0.8.1-pre rev 5445 on Mac (OS 10.9.5) and would like to validate waters. However, after selecting the criteria and hitting 'Ok', the terminal only gives me (command-in-path-or-absolute? *probe-command*) Interestingly, all the

Re: [COOT] Was: problems with validate waters, Now: X11 on Mac

2014-11-20 Thread Paul Emsley
On 20/11/14 16:48, Tobias Beck wrote: Hi Paul and Huw, Thanks for your emails. That is all I get in the terminal too (Coot 0.8.1-pre rev 5423 on OS X 10.9.5) but the table of “Questionable Waters” does appear (hidden underneath the main window). Is that not happening for you? X11 window

Re: [COOT] Ramachandran maps

2014-12-09 Thread Paul Emsley
On 09/12/14 14:47, PC wrote: Hi guys, Sorry for the repost in COOT/CCP4/PHENIX. It is possible on of the users in one of these communities might know the answer I was wondering if there is a small script I can use to generate the outline of the allowed regions of Ramachandran map on to which

[COOT] Coot 0.8.1

2014-12-15 Thread Paul Emsley
We are pleased to announce Coot Release 0.8.1. (Basically a bug-fix release.) Redhat, CentOS, OpenSuse and Ubuntu binaries will appear here shortly: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/ WinCoot here hopefully:

Re: [COOT] Reordering chains in a pdb file

2015-01-20 Thread Paul Emsley
On 20/01/15 16:53, Rex Palmer wrote: My protein has 4 separate chains A,B,C and D but the pdb file has the chains in order C,D,A,B. Is there any existing software that would rearrange my pdb file as A,B,C,D? Extensions - Modelling - Reorder chains. This should work in 0.8 and 0.8.1, but

Re: [COOT] Changing carbon bond colours... (when coloured by chain)

2015-01-21 Thread Paul Emsley
On 19/01/15 14:56, Christoph Parthier wrote: Hi, I noticed when adjusting the 'bond colours' using the slider in 'Edit/Bond Colours...' when an molecule (1 chain) is 'coloured by chain') with activated check mark 'Change colours for Carbons only' only the colours of the first chain (chain A)

Re: [COOT] UNDO-Bug in C-alpha Baton Mode (Coot/WinCOOT)

2015-01-21 Thread Paul Emsley
On 19/01/15 14:45, Christoph Parthier wrote: Hi, I know the 'baton building' feature of COOT is rarely used, but - believe it or not - we use it in teaching quite a lot and there is a bug which every time results in desperate students (and supervisors...), so high time to report: Once 'Ca

Re: [COOT] WARNING:: Failed to find restraints for :CL:

2015-01-30 Thread Paul Emsley
On 30/01/15 18:14, Murpholino Peligro wrote: hello everybody! Hello Murpholino Peligro, I was just getting a better structure from the 193L.pdb with coot (Fetch PDB and map using EDS) Everything was ok,...but the last residue (129) could not be refined ...The warning that appeared was

Re: [COOT] Peak Pick coordinates.

2015-01-25 Thread Paul Emsley
On 24/01/15 17:11, Kenneth A. Satyshur wrote: Is it possible to output a list of peak pick coordinates? I want the top 100 peaks in a list so I can display them and determine if I want to keep them or not. (list-head (reverse (map-peaks imol 2) 100)) HTH, Paul.

Re: [COOT] displaying one alternate conformation at a time

2015-01-06 Thread Paul Emsley
On 21/12/14 21:37, Scott Horowitz wrote: Hi all, Is it possible to display only one alternate conformation at a time? I have a situation where I have several alternate conformations, and it's hard to see with them all displayed at the same time. Hi Scott, No it's not - sorry. You might

Re: [COOT] GTK warning

2015-01-14 Thread Paul Emsley
On 14/01/15 05:13, Satyabrata Das wrote: Thank you for this kind reply, the font sizes are not much but they are bold, however sometime they are normal, please see the attached image. Dear Satyabrata, It looks like you are using a binary built by CCP4. Do you see the same problem with

Re: [COOT] GTK warning

2015-01-12 Thread Paul Emsley
On 12/01/15 15:49, Marcin Wojdyr wrote: Dear Satyabrata, I think the gtk messages can be ignored. They can be ignored. I don't know why you are seeing them. How the bold fonts look like? Like this:

Re: [COOT] r5551 issue

2015-02-09 Thread Paul Emsley
On 08/02/15 16:43, Gabriele Balducci wrote: hello, while building r5551 from source, I get the following error: 8888 In file included from phenix-geo.hh:3:0, from phenix-geo.cc:6: ../coot-utils/residue-and-atom-specs.hh:37:19: error: 'mmdb' has not been

Re: [COOT] Problem loading EM .mrc map

2015-02-18 Thread Paul Emsley
On 18/02/15 23:31, Tc Cheng wrote: Hi all, Hi Tc, Happy goats? I am currently using coot 0.8.2 pre-release on Centos 5. good for you! I have a ~ 4.4A EM map OK! Not bad! (in mrc format) that I want to build a model in coot. OK! The map shows up properly in chimera but not in

Re: [COOT] How to change directory sorting?

2015-03-19 Thread Paul Emsley
On 17/03/15 14:10, Peter Stogios wrote: Hello, In Coot's directory/file open dialog window when opening any file type, the directory sorting doesn't make any sense and I cannot find what directory I need without pulling teeth. Directories are not sorted directories by name, date modified,

Re: [COOT] molecule rubber banding not working in 8.1

2015-03-11 Thread Paul Emsley
On 11/03/15 00:06, Kenneth Satyshur wrote: After using 7.1 for a while, it was easy to 'real space refi zone' a amino acid. Pull on it and it will drag everything else with it. On 8.1 when I try this, it just rips an atom away from the residue and does not move the whole residue. There

Re: [COOT] coot validation keywords

2015-03-12 Thread Paul Emsley
On 09/03/15 11:47, Andrea Ilari wrote: I changed the operating system automatically from ubuntu 12.04 to Ubuntu 14.04. My version of COOT is still working but the validate routine doesn't work properly, I can't open the ramachandran plot, the geometry analysis .. and also the HID scrollwheel,

Re: [COOT] RSR behavior in coot 0.8.1

2015-03-24 Thread Paul Emsley
On 24/03/15 22:01, Roberts, Sue A - (suer) wrote: I'm wondering why this was changed. Does the optimum elasticity change with resolution, map quality, or another experimental limitation? Or does it more of a user preference? Because cis-peptides. My worry was that in the previous regime, it

Re: [COOT] PDB parsing in coot 0.8.1 versus prior versions

2015-03-31 Thread Paul Emsley
be the issue here? Cheers, Jose On 03/27/2015 07:13 PM, Paul Emsley wrote: On 25/03/15 22:27, nih\mayerm wrote: Deal Paul. Recently I had an unusual case of dual occupancy of a ligand binding site by two different ligands. I refined this by giving same resids to the two ligands (here C1

Re: [COOT] Reading multichart script into WInCoot.

2015-03-28 Thread Paul Emsley
On 28/03/2015 15:47, Ian Tickle wrote: On 27 March 2015 at 19:16, Paul Emsley pems...@mrc-lmb.cam.ac.uk mailto:pems...@mrc-lmb.cam.ac.uk wrote: There might be a python version of these available from the Molprobity server. It should be straightforward for them to make

Re: [COOT] Copy NCS residue range

2015-03-04 Thread Paul Emsley
Sorry for the late comment, I somehow missed this while I've been away. Yes, this is very horrible - and noted by Airlie last year. It's on the Must-Fix list for 0.8.2. Paul. On 23/02/15 09:24, Phil Evans wrote: So why is the option to change it presented in the dialog? You can change it

Re: [COOT] Reading multichart script into WInCoot.

2015-03-27 Thread Paul Emsley
On 27/03/15 17:04, Ian Tickle wrote: Hello All I'm trying to read the script from multichart into WinCoot. I do: multichart-coot reduce.pdb reduce.scm but when I select Calculate - Run Script absolutely nothing happens, there's no error message on the console, nothing. Hmm... that needs

Re: [COOT] PDB parsing in coot 0.8.1 versus prior versions

2015-03-27 Thread Paul Emsley
On 25/03/15 22:27, nih\mayerm wrote: Deal Paul. Recently I had an unusual case of dual occupancy of a ligand binding site by two different ligands. I refined this by giving same resids to the two ligands (here C1 in coordinates below), refining their occupancy (in Phenix) - worked very well.

Re: [COOT] Ligand density fit scores

2015-04-30 Thread Paul Emsley
On 28/04/15 10:41, Lau Sze Yi (SIgN) wrote: Hi, I fitted small molecule ligand into observed electron density using the Find Ligands function and did a density fit analysis. What is considered an acceptable score? You want a density correlation of greater than 0.89 to be better than the

Re: [COOT] Edit bond colours in COOT

2015-04-30 Thread Paul Emsley
On 23/04/15 23:13, Marie Elizabeth Fraser wrote: Hello, Is there a way to change the bond colour for the second (or subsequent) chain in a PDB file when the models are represented as Calphas? I use Edit Bond Colours to change the colour of the carbon atoms, so that the first subunits

Re: [COOT] 'Add parallel planes restraint'

2015-04-30 Thread Paul Emsley
On 22/04/15 15:17, Andreas Schedlbauer wrote: Would like to know how the new feature in coot 0.8 'Add parallel planes restraint' (Extensions/Modules/User defined restraints) really works. If defined does not seem to have any effect in real space refinement. The method is described here:

Re: [COOT] FW: New ligand 3-letter code (help-7071)

2015-06-23 Thread Paul Emsley
It seems to me that Rachel's answer is somewhat unclear. To rephrase then: if I deposit a new structure with a new ligand and I give it an as-yet-unassigned three-letter-code, will the RCSB/wwPDB keep the code I gave it? Actually a straight reading of Rachel's answer is no - but I

Re: [COOT] sequence viewer broken for long chans.

2015-06-14 Thread Paul Emsley
On 13/06/15 18:12, Oliver Clarke wrote: I realize this is somewhat of a niche concern, but figured I would report it anyway. The sequence viewer is broken for long protein chains, it doesn't show anything after residue 2241. No, it's not broken - there is a limitation in the X11 window

Re: [COOT] New ligand 3-letter code

2015-06-14 Thread Paul Emsley
On 05/06/15 14:50, Sheriff, Steven wrote: At BMS we do many hundreds of structures a year with ligands and we assign the same, already assigned, three-letter code for all of our ligands (unless we have two or more different ligands in a single structure...) (I have plans to improve

Re: [COOT] PyMOL v. Coot map 'level'

2015-06-01 Thread Paul Emsley
On 29/05/15 21:15, Emilia C. Arturo (Emily) wrote: Hello. I am struggling with an old question--old because I've found several discussions and wiki bits on this topic, e.g. on the PyMOL mailing list (http://sourceforge.net/p/pymol/mailman/message/26496806/ and

Re: [COOT] Dragged refinement fails with riding hydrogens

2015-05-28 Thread Paul Emsley
On 27/05/15 16:16, Oliver Clarke wrote: Hi all, dragged refinement doesn't seem to work for structures with riding hydrogens - see linked screen recording showing dragged refinement of the same structure with and without hydrogens.

Re: [COOT] Negative positive contours for neutron map.

2015-05-24 Thread Paul Emsley
On 24/05/2015 16:57, Ian Tickle wrote: Hello, does anyone know how to simultaneously display negative positive contours for a neutron 2Fo-Fc map? For example, as in Fig. 2 here:

Re: [COOT] Core dump on Glycan addition.

2015-07-09 Thread Paul Emsley
On 09/07/15 13:38, David Briggs wrote: Dear all, We have encountered some problems when using the carbohydrate module in coot. When I centre on an Asn which has NAG density, invoke the Carbohydrate module and select Add ASN-NAG NAG, Coot crashes and dumps the core. Dear David, Thank you

Re: [COOT] pdb file problem with duplicate amino acid

2017-02-01 Thread Paul Emsley
On 31/01/2017 20:09, Dale Tronrud wrote: On 1/31/2017 11:51 AM, Paul Emsley wrote: On 31/01/17 17:54, Edwin Pozharski wrote: Whatever the rationale was, there is a structure in the PDB that has alternate conformer of a residue listed with different residue type - A is arginine and B

Re: [COOT] auto open MTZ problem

2017-01-31 Thread Paul Emsley
On 31/01/17 13:26, mesters wrote: Hi, I currently run ccp4 version 7.0.028 on a Mac Air with OS X 10.11.6 and experience no problems if start Coot from within qtRView (model and maps are displayed correctly) If a start Coot by itself and load a PDB model and then use "auto open MTZ" and

Re: [COOT] model with most likely rotamers

2017-02-06 Thread Paul Emsley
On 06/02/2017 08:45, Tim Gruene wrote: I would like to create an artificial PDB model (starting from an existing one) where every side chain is replaced with the most likely rotamer. I do not care about clashes at this stage. Can this be scripted with Coot? Yes. Iterate through the residues

Re: [COOT] Refining RNA into low res maps

2017-02-07 Thread Paul Emsley
On 07/02/17 16:58, Jonathan Grimes wrote: is there a way of refining dsRNA into low res maps (6-8A) …obvious major and minor grooves…. where the base pairs are restrained but the dsRNA can curve…. ive used coot to make dsRNA and made the 2 strands …one chain ID….. Take a look

Re: [COOT] many copies of protein chain, coot slow

2017-01-30 Thread Paul Emsley
On 30/01/2017 23:02, Jan Abendroth wrote: I am refining a protein with 16 copies of the same chain per ASU. Fortunately, it is a small protein. Coot has become really slow for this structure. Any real space refinement or placement of a water makes coot for 10+ seconds unresponsive. The coot

Re: [COOT] Highlight and color chain breaks

2017-01-26 Thread Paul Emsley
On 26/01/2017 22:23, Oliver Clarke wrote: Hi all, I wrote a little jiffy to highlight missing segments and color by length (breaks with <15 missing residues are gray; 16-50 orange; and 51+ red). It is included in this script (https://www.dropbox.com/s/0b4bebwxw0p9x0e/oli_custom.py?dl=0), and

Re: [COOT] rotate/translate zone

2017-01-23 Thread Paul Emsley
On 23/01/17 16:29, Susana GONCALVES PIRES wrote: Hello everyone, maybe this question came out already, but I would like to know if there is a way to do "rotate/translate zone" of several chains at the same time? If you want to rotate/translate zone on several chains (A,B,C), but not the

Re: [COOT] Faster delete zone?

2017-01-23 Thread Paul Emsley
On 23/01/17 15:40, Oliver Clarke wrote: Hi, Delete zone (delete_residue_range()) is extremely slow when deleting large selections, often taking many minutes to delete a single large chain, even when backups are disabled. Is there an alternative function that is faster, or the possibility of

Re: [COOT] user-defined-restraints

2016-09-28 Thread Paul Emsley
On 28/09/16 10:51, Matzov Donna wrote: Hello, Hello Donna, For RNA modelling I used to have a "user-defined-restraints.scm" script which allowed me to maintain proper base-paring geometry while I did real-space refinement and regularization. Unfortunately, my script doesn't seem to work on

[COOT] Release 0.8.7

2016-11-08 Thread Paul Emsley
Coot 0.8.7 is released. Binaries and source code from http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot For those who compile from source, this version works with CCP4SRS (not currently enabled in my standard binary builds). Release 0.8.7 o FEATURE: Lidia now has canvas scaling o

Re: [COOT] fresh coot misbehaves? (well, not really)

2016-11-10 Thread Paul Emsley
On 11/11/2016 03:32, Edwin Pozharski wrote: I had an opportunity to build coot executable on a fresh ubuntu box. It compiles fine after you install few dependencies but I noticed the following: 1) it seems that coot won't work without CCP4. "Without CCP4" is slightly ambiguous. Let's

Re: [COOT] colour coding map values on molecular surface

2016-11-04 Thread Paul Emsley
On 04/11/2016 15:55, Tim Gruene wrote: I would like to draw the surface of a (small) molecule, e.g. at VdW-radius, and display by colour the map values from an mtz-file at the surface. There is no interface to do this. Ideally I would like to set surface distance from the nuclei, the

Re: [COOT] proline RSR problems

2016-10-12 Thread Paul Emsley
On 12/10/2016 13:43, Kevin Jude wrote: I am frequently getting distortions of proline residues during real space refinement - specifically, close approaches between C and CD (pictured). It's hard to nail down exactly what is happening but it seems like planar peptide restraints aren't working

Re: [COOT] Edit Chi Angle crash

2017-01-13 Thread Paul Emsley
On 11/01/2017 10:10, Luca Pellegrini wrote: The ‘Edit Chi Angle’ command makes Coot crash (the Coot window implodes), the instant I start adjusting manually the side chain. This only happens when I launch Coot by double-clicking its icon; when I run it from a terminal window, with

Re: [COOT] C-alpha baton mode not working anymore in 0.8.7

2017-01-13 Thread Paul Emsley
On 13/01/2017 10:10, Christoph Parthier wrote: Since version 0.87 starting C-alpha baton building (after map skeleton creation) crashes COOT. In version 0.86 it still worked. Occurs in Coot for Windows and Linux (Scientific Linux 6.7). dictionary-related again, I guess. We use the c-alpha

Re: [COOT] Coot crashing after "Add OXT terminal" revision 6498

2016-12-02 Thread Paul Emsley
On 30/11/2016 10:25, Folmer Fredslund wrote: As was mentioned, there were some problems with COOT and mutations after a recent CCP4 update. I've seen crashes after "Add OXT to Residue..." (from Calculate->Other Modelling Tools) in revision 6498 provided by CCP4-7.0 (update 24), but I don't see

Re: [COOT] stuck with black fonts

2016-12-02 Thread Paul Emsley
Quite Right Folmer, I am pretty sure that this was fixed in 0.8.2: Release Notes has this item: o BUG-FIX: Resetting of Own font colour on opening the preferences dialog fixed. Paul. On 02/12/2016 10:45, Folmer Fredslund wrote: Dear Andrea, I would suggest, if at all

Re: [COOT] pre-proline peptide restraints

2016-12-02 Thread Paul Emsley
ut this problem in the "right" COOT way? It sounds that you are thinking the right thoughts. I'm not sure about the details for the particular problem though... perhaps a cis-model for a cis pre-Pro that won't stay cis? Paul. On Mon, May 23, 2016 at 3:28 PM, Paul Emsley <pems...

Re: [COOT] Unnatural AA

2017-01-06 Thread Paul Emsley
On 05/01/2017 17:52, Luca Pellegrini wrote: I have created an unnatural amino acid (ua1.pdb, ua1.cif) in JLigand, I have added it to my structure and fitted it into the density. Now how do I tell Coot, when I regularise the local structure, to keep the peptide bond stereochemistry with the

Re: [COOT] including symmetry mates in sphere refinement

2016-12-19 Thread Paul Emsley
On 19/12/2016 08:44, Andrea PICA wrote: Hello everyone, I was wondering whether it would be possible in coot to include symmetry related atoms in sphere refinement. I've thought about it. It's tricky and probably slow. It's a nice feature to have, but not scheduled at the moment. Paul.

Re: [COOT] Problem doing real-space refinement of MSE residue

2017-03-24 Thread Paul Emsley
On 23/03/2017 17:55, Mark Saper wrote: I have a situation where I manually edited my PDB file to rename MET to MSE, then made the appropriate change to change all “ SD" atoms in MSE to “SE “. When I optimize the geometry with Real Space Refine Zone, the amide proton (H) moves several Å way

Re: [COOT] Coot scripts moved to github

2017-03-09 Thread Paul Emsley
On 08/03/17 21:36, Oliver Clarke wrote: Hi all Someone pointed out to me on twitter that my coot scripts website had died (because tiddlyspace is sadly no more). I'm keeping an up-to-date version of my extra bits and pieces on github: https://github.com/olibclarke/coot-trimmings/ If they

Re: [COOT] SSM output

2017-03-10 Thread Paul Emsley
On 10/03/2017 12:43, Bernhard Rupp wrote: is there a way to redirect the SSM Superpose output from the console to a file? Or is there a log file already? I’d like to simply read the per-residue list from the console window for plotting purposes. Hi Bernhard, There is not a special

[COOT] Coot-0.8.8 released

2017-03-13 Thread Paul Emsley
We are pleased to announce the release of coot-0.8.8. Binaries and source code from http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot Release 0.8.8 o FEATURE: C++11 compilers will multi-thread multiple map contouring o FEATURE: SMILES -> simple 3D menu item added o CHANGE:

Re: [COOT] List of solvents

2017-03-04 Thread Paul Emsley
Hi Bernhard, On 04/03/2017 14:28, Bernhard Rupp wrote: where can I modify/preserve (in my preferences probably) the list of solvent molecules appearing as pre-selected in the “Solvent models added to molecule” panel that appears from Extensions/Modelling/Add other Solvent? Yes you can.

Re: [COOT] Changing scroll map keybinding

2017-07-12 Thread Paul Emsley
On 12/07/2017 09:34, Jan Stransky wrote: Hi, I believe, I have seen somewhere a keybinding, which cycle through maps attached to scroll wheel (basicaly moving the radio button "Scroll" in Display Manager). However, I can't find anywhere what key does that... Any ideas? Or do you know a coot

Re: [COOT] rev 6782: $(SQLITE3_LIBS) link missing in some Makefile.am files?

2017-06-19 Thread Paul Emsley
On 19/06/17 10:08, Gabriele Balducci wrote: hello paul and coot developers while building rev 678{1,2}, I get the following errors (actually, the error is the same at three different points in sequence during the build): ---8<---

Re: [COOT] Coot-0.8.7 slow in Debian

2017-05-20 Thread Paul Emsley
It's nothing to do with Coot binaries and everything to do with the graphics drivers. If it's the font that's the issue, I think that (after discussion with Marcin) I had a work-around once, but it seems to have been dropped. Maybe I can find it and conditionally compile it for Debian.

[COOT] SPAM [was Re: DHL ONLINE SHIPPING PREALERT ADVISORY]

2017-05-24 Thread Paul Emsley
Sorry about that, I'll try and clean it up. P.

Re: [COOT] Coot-0.8.7 slow in Debian

2017-05-21 Thread Paul Emsley
On 21/05/2017 13:17, Phong Nguyen wrote: Yes I think it is the problem of the version of Coot for Debian on the website. The version of Coot that in CCP4 package works well on my computers As I said, it's not to do with the version of Coot, it's to do with the graphics drivers. If you want

Re: [COOT] add_alt_conf function

2017-06-02 Thread Paul Emsley
On 02/06/2017 15:00, Kempf, Georg wrote: Hi all, I wanted to use the function /add_alt_conf/*(*imol, chain_id, res_no, ins_code, alt_conf, rot_no); sample: add_alt_conf(0, “A“, 1, ““, ““, 1). However, although giving a number in case of rot_no, the rotamer selection dialog still pops up when

Re: [COOT] turn off auto recentring?

2017-09-06 Thread Paul Emsley
On 06/09/2017 18:30, Kenneth Satyshur wrote: Me too. But I can't read the reply because I don't know how to read a .scm file. Can you send as a pdf? OK... For the record a .scm or .py file should be read as plain text. Paul. advancing-labels.pdf Description: Adobe PDF document

Re: [COOT] navigating back to the ligand

2017-09-06 Thread Paul Emsley
On 06/09/2017 18:22, Paul Emsley wrote: Similar case for ligands...the ligand button short cut is pretty good, but if I navigate off the ligand to look at surroundings, the next click of the heteroatom /ligand center button will likely have reset to the top of the list, and with cofactors

Re: [COOT] correct protonation state in His side chain

2017-09-13 Thread Paul Emsley
I don't think that that's what Xiao Lei means. I think that Xiao Lei refers to the problem of assignment of rotamer, tautomer and ionisation state described here: https://www.chemcomp.com/journal/proton.htm Coot can't do that (yet). Regards, Paul. On 13/09/2017 02:27, Murpholino Peligro

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