[PyMOL] Selecting specific ligands for colouring

Hi, I know I must be getting annoying, although I must say this mailing list and its users have been very helpful for me so thank you all. My question this time is how do I select specific ligands? Like I am using PDB ID 2HYY and I'd like to set the imatinib (STI600) ligand as the only visibl

Re: [PyMOL] Selecting specific ligands for colouring

Hi Brenton, It seems 2HYY only has that one (type of) ligand present? so: fetch 2hyy as cartoon show sticks, organic color black, elem c and organic remove not chain a gives me a cartoon representation of the protein, with a stick representation of the ligand. There are 4 copies of the complex i

[PyMOL] Scripting attempts

Hi, I've been executing the pml script I wrote: set ray_opaque_background, 0 png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1 for i in range(2, 60) rotate y, 6 png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY

Re: [PyMOL] PyMOL png movie creation from command line

Hi, When you ray trace you can specify the dimensions of the resulting image in pixels, eg: ray 600,800 You can also set the resolution when saving the png file: png image.png, dpi=300 HTH, Matt Baumgartner On 01/06/2015 12:39 AM, Brenton Horne wrote: > Hi, > > I'd like to know how to create a

Re: [PyMOL] Selecting specific ligands for colouring

Hi, I just wanted to chime in and add to what Folmer said. Your selection syntax was close, but not quite correct, you are missing a slash. Following you example, you would do /2hyy//A/600 where 600 is the residue id of the ligand. But in general, I would recommend using the syntax that Folmer

Re: [PyMOL] Scripting attempts

(a) I'll let someone else say whether you can use range in pml files, not completely sure on that one and the formatting rules. personally, I would write this in python, and you would need a : after the range (b) you are missing any indication of what %4d refers to. See example 3.23 on http://www.

Re: [PyMOL] Scripting attempts

Hi, You may need to use the API instead of the command. cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300, ray=1) Matt Baumgartner On 01/06/2015 10:01 AM, Brenton Horne wrote: > Hi > > I received this error from y

Re: [PyMOL] Scripting attempts

Hi :) You can use for-loops in pml files, but it's a bit tricky. Usually you will want to enclose the code in a python .. python end block, indicating that the lines are pure python: python for i in range(2,61): ... python end Also mind that range runs UP TO (excluding) the last number, so you

Re: [PyMOL] Scripting attempts

Is it in your for loop? for i in range(2,61): rotate y, 6 cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300, ray=1) On 1/6/15, 10:13 AM, Brenton Horne wrote: > That gave the error: > > cmd.png("C:\Users\

Re: [PyMOL] Scripting attempts

Be sure to reply to the list so everyone can benefit from the questions and answers. Ah, as Tsjerk mentioned, you need to wrap it in a python-python end block. set ray_opaque_background, 0 png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - imatinib\PyMOL movie\Image0001.png, dpi=300

Re: [PyMOL] Scripting attempts

Hey :) "Image{}.png".format(str(i).zfill(4)) can also be written Image{:04d}.png".format(i) Cheers, Tsjerk On Tue, Jan 6, 2015 at 4:52 PM, Matthew Baumgartner wrote: > Be sure to reply to the list so everyone can benefit from the questions > and answers. > > Ah, as Tsjerk mentioned, you ne

Re: [PyMOL] Scripting attempts

I think that the problem is that python is interpreting part of your directories as special characters. This is due to the fact that Windows uses the backslash as the directory separator which is also a special character in python (and in *nix systems). In a regular python terminal, if I do:

Re: [PyMOL] Dot representation

Thanks Jared. On Mon, Jan 5, 2015 at 1:35 PM, Sampson, Jared wrote: > Hi Yarrow - > > 1. Yes, according to the wiki , the > dots are located on the vdW surface unless the `dot_solvent` setting is > turned on (in which case they’re on the solvent accessi

Re: [PyMOL] Scripting attempts

Hi Brenton, I'm pretty sure you have to import python in your script. Otherwise the python commands will be ignored. Also you forgot to put colons after your 'for' statement. Either way, I think pymol got the first image then ignored the 'for statement' and just went straight to the second 'png...

Re: [PyMOL] Scripting attempts

Sorry, I didn't read the other entries. Thanks for the "python end" code. I have had this problem with loops a lot in pymol and this solves it. -Yarrow On Tue, Jan 6, 2015 at 9:21 AM, Yarrow Madrona wrote: > Hi Brenton, > > I'm pretty sure you have to import python in your script. Otherwise th

[PyMOL] How do I undo my last command I executed in the PyMOL command line and viewer?

Hi, I thought that running "undo" from the PyMOL command line would do this but it didn't do anything that I could see visually in the viewer. I've also tried going to Edit->Undo and it didn't do anything visually apparent in the viewer. Thanks for your time, Brenton -

Re: [PyMOL] holes in isosurface representation

Hey Jacob, Are Lagging_A and Leading_B selections or objects? Generally for surfaces to display right you have to create a new object for the part you want (using either the create or extract commands). Otherwise you get holes in the surface where the selection contacts the rest of the object. -S