[COOT] Coot from terminal / Coot from icon

Hi there. A friend of mine has a problem with coot 0.7.2. the one that is installed with the ccp4i suite. She's using Ubuntu 14.04. (I have the same installation in Fedora 20 (and because by default there are no icons in the desktop, then I suppose that's why I haven't encountered the problem))

[COOT] get difference map peak values

Hi everybody. Can I get difference map peak values with a single click? (clicking on a negative/positive density) How? (I think I read this somewhere, but google or looking at the mailing list is not helping) Thanks

Re: [COOT] get difference map peak values

precise number then with this way is nonsense anyway, because the map numbers change with every refmac5/phenix.refine run. Jan On 11/04/2014 01:31 AM, Murpholino Peligro wrote: Hi everybody. Can I get difference map peak values with a single click? (clicking on a negative/positive density

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

Just an opinion For me it's more difficult to do real space refinement in coot 8.1 than in the 7.1 version. (I do not have the problem of breaking residues) And mmm...just to wanted to ask if..this was due to a parameter that changed between the different versions...or maybe is just me?

Re: [COOT] key binding to toggle maps

Hi... I was looking for something like this... but I want to switch between maps...say I have my blue map, my red/green map and my anomalous mapcan I switch between them...scroll to desire rmsd and change to the other map... (I scroll a lot these three maps while doing model building...)

[COOT] open lots of ccp4 maps in coot with a color range

Hi Is it possible open 30 maps in red-ugly to red-bright? and the next 30 maps in green-ugly to green-bright? So I can have in total 60 maps over my structure in different shades of green and red... Thanks a lot

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

Not sure if coot, but maybe molprobity can help. http://molprobity.biochem.duke.edu/help/reduce_guide/reduce_guide.html 2017-09-12 19:10 GMT-05:00 Xiao Lei : > Dear All, > > Can I correct protonation state in His side chain in Coot? >

Re: [COOT] what's the difference between ccp4's coot and a normal coot?

ot set this, the shifting can get very slow with > some graphics cards, in case an atom label is displayed. > > Best, > Tim > > On 06/06/2018 08:25 PM, Murpholino Peligro wrote: > >> @MW: `bzr checkout bzr+http://oisin.rc-harwell.ac.uk/bzr/series-70/trunk >> <

Re: [COOT] what's the difference between ccp4's coot and a normal coot?

: > On 07/06/2018 15:45, Murpholino Peligro wrote: > >> Dear all. >> Putting this line >> (set-use-stroke-characters 1) >> into >> ~/.coot-preferences/coot.scm >> fixes the slowness. >> > > OK, interesting. > > >> I wonder whe

Re: [COOT] what's the difference between ccp4's coot and a normal coot?

@MW: `bzr checkout bzr+http://oisin.rc-harwell.ac.uk/bzr/series-70/trunk devtools` gives me bzr: ERROR: Not a branch: "bzr+http://oisin.rc-harwell. ac.uk/bzr/series-70/trunk/". @PE: I mean graphically and I guess computationally. Check out the videos!!

Re: [COOT] what's the difference between ccp4's coot and a normal coot?

GMT-06:00 Paul Emsley : > > On 06/06/18 19:25, Murpholino Peligro wrote: > > @MW: `bzr checkout bzr+http://oisin.rc-harwell.ac.uk/bzr/series-70/trunk > devtools` gives me > bzr: ERROR: Not a branch: "bzr+http://oisin.rc-harwell.a > c.uk/bzr/series-70/trunk/". > @PE:

[COOT] superpose coordinates and then maps

Hi all I have two coordinates (A.pdb & B.pdb) along with their respective maps (A.mtz, B.mtz). I would like to superpose A with B. Can somebody explain in detail how to achieve this in coot? I know how to do it in pymol ( https://pymolwiki.org/index.php/Matrix_Copy)...then I export maps and pdbs

Re: [COOT] removing dotted lines

Dear Kenneth. For this to work you need to do: Calculate->Scripting -> Python and then write set_draw_missing_residues_loops(0) (in the window that emerges) and then press enter. I am attaching your message below and adding this to the coot mailing list just in case someone else does not find the

Re: [COOT] removing dotted lines

https://pemsley.github.io/coot/blog/2020/06/25/turn-off-missing-loops.html set_draw_missing_residues_loops(0) El mié, 3 de nov. de 2021 a la(s) 09:18, Thomas, Leonard M. (lmtho...@ou.edu) escribió: > Hello, > > Just a quick question, is there an easy way to toggle off and on the lines >

Re: [COOT] coot not loading cif files

Have you tried File-> Open Coordinates... (that says in a little yellow box 'pdb, cif or shelx res format')? El mié, 9 feb 2022 a la(s) 15:03, Gabby Budziszewski (budzi...@unc.edu) escribió: > I am running coot 0.8.2 on MacOS Catalina 10.15.7. > > I am primarily a GUI user. > > I am having

[COOT] default colors?

How do I change the default colors in coot? for all three maps, the "normal" density, the difference map and the anomalous map? Thanks To unsubscribe from the COOT list, click the following link: