Re: [COOT] Slow coot built from source - Mesa???

2014-03-11 Thread Ethan Merritt
On Tuesday, 11 March 2014 07:48:18 PM Ethan Merritt wrote: > On Tuesday, 11 March 2014 07:29:50 AM Paul Emsley wrote: > > > > The font rendering of Coot has been niggling me for a while. I have > > noticed a slowdown in the FPS when labels are added, but not perhaps as > > much as you suggest.

Re: [COOT] Slow coot built from source - Mesa???

2014-03-11 Thread Ethan Merritt
On Tuesday, 11 March 2014 07:29:50 AM Paul Emsley wrote: > On 11/03/14 06:29, Ethan A Merritt wrote: > > On Sunday, 02 March, 2014 16:17:22 Ethan Merritt wrote: > >> I recently acquired a new machine and found that my previous > >> coot executables will not run on it, and neither will the > >> stab

[COOT] Delete chain

2014-03-11 Thread Oliver Clarke
Another one to chalk on the list of things that would be nice to have but not really needed - I feel like having a delete chain option in the ‘Delete item’ dialog would be very handy… I often find myself needing to delete a chain (from a complex or oligomer for example), and I always switch th

[COOT] Blank chain IDs on newly placed helices

2014-03-11 Thread Oliver Clarke
Hi all, A couple of minor bugs/queries... I’ve noticed in the past few daily builds that newly placed chain IDs have a blank chain ID… I’m not sure whether this is deliberate or a bug, but I don’t remember it being that way before? Perhaps defaulting to A might be better, in case other program

[COOT] Sharpening slider is slow on large maps

2014-03-11 Thread Oliver Clarke
Hi all, I guess this is more of a feature suggestion than anything - I do not know how hard it is to implement. I really like the on-the-fly adjustment of map sharpening implemented in coot. However, for large maps I find I have to use the scripting interface to change the sharpening factor,

Re: [COOT] phi/psi angles

2014-03-11 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Great! Thanks a lot, Andrew! Cheers, Tim On 03/11/2014 02:04 PM, Andrew Leslie wrote: > Hi Tim, > > CCP4 program ANGLES will compute phi,psi for you, is this helps. > > Andrew > > > On 11 Mar 2014, at 11:13, Tim Gruene > wrote: > >> Hello all,

Re: [COOT] phi/psi angles

2014-03-11 Thread Andrew Leslie
Hi Tim, CCP4 program ANGLES will compute phi,psi for you, is this helps. Andrew On 11 Mar 2014, at 11:13, Tim Gruene wrote: > Hello all, > > is it possible to get a listing of all phi/psi angles in the peptide? > When I click on the Ramachandran plot they are printed to the console - > how t

Re: [COOT] phi/psi angles

2014-03-11 Thread Paul Emsley
On 11/03/14 11:13, Tim Gruene wrote: is it possible to get a listing of all phi/psi angles in the peptide? When I click on the Ramachandran plot they are printed to the console - how to I get the entire list non-interactively? Hi Tim, I've been wanting to add this for a while. But it's not d

[COOT] phi/psi angles

2014-03-11 Thread Tim Gruene
Hello all, is it possible to get a listing of all phi/psi angles in the peptide? When I click on the Ramachandran plot they are printed to the console - how to I get the entire list non-interactively? Cheers, Tim -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen

Re: [COOT] different results for finding waters from within coot or on the cmd line

2014-03-11 Thread Michael Engel
Dear Tim, good point. I have checked for duplicate installations and there is indeed a second one from the ccp4 6.4.0 tree which hasn't precedence in the path. Neverthless I have checked it out and it gives the same result. Many thanks, Michael On 11 March 2014 09:53, Tim Gruene wrote: > Dear

Re: [COOT] different results for finding waters from within coot or on the cmd line

2014-03-11 Thread Tim Gruene
Dear Michael, did you also check you are using the same binary? You might be using findwaters from the CCP4 tree on the command line and from within the coot-tree when using coot, in case you installed coot separately on top of ccp4 (or maybe phenix?). Best, Tim On 03/11/2014 08:14 AM, Michael E

Re: [COOT] different results for finding waters from within coot or on the cmd line

2014-03-11 Thread Michael Engel
Hi Paul, thanks for your quick response. On 11 March 2014 08:38, Paul Emsley wrote: > On 11/03/14 07:14, Michael Engel wrote: > >> I can't reproduce the results I get by using find waters from within coot >> when running findwaters on the command line on the same pdb/mtz. I have >> double chec

Re: [COOT] different results for finding waters from within coot or on the cmd line

2014-03-11 Thread Paul Emsley
On 11/03/14 07:14, Michael Engel wrote: I can't reproduce the results I get by using find waters from within coot when running findwaters on the command line on the same pdb/mtz. I have double checked all the command line switches are the same and compared the output in the log files. Nothing

Re: [COOT] Slow coot built from source - Mesa???

2014-03-11 Thread Paul Emsley
On 11/03/14 06:29, Ethan A Merritt wrote: On Sunday, 02 March, 2014 16:17:22 Ethan Merritt wrote: I recently acquired a new machine and found that my previous coot executables will not run on it, and neither will the stable or "nightlies" built for Fedora/RHEL or Ubuntu. No problem, I thought, I

[COOT] different results for finding waters from within coot or on the cmd line

2014-03-11 Thread Michael Engel
Hi, I can't reproduce the results I get by using find waters from within coot when running findwaters on the command line on the same pdb/mtz. I have double checked all the command line switches are the same and compared the output in the log files. Nothing obviously different but I am getting