A similar thing happen in 3d software where generic .Obj files do not have any information of material analogous to colors in this case. They bypass this limitation by having a software specific saving file format containing all information or a separate file for material. In pymol phool scripting file can help stor coloring informatiomation for the molecules as it is highly unlikely to store color information in its generic pdb/cif format. In another approach such information can be hidden in comments in specific format that pymol would develop to parse on load event.
On Thu, 27 Jun 2019, 20:09 Sarameri, Jesse, <jesse.saram...@helsinki.fi> wrote: > Hello, > > > That might also explain why the same molecule loaded in LiteMol gives > different colouring. > > So the conclusion is that the colors are not defined in molecules but > instead in programs > > that displays them. > > > Thank you! > > > Regards, > > Jesse Sarameri > > > ------------------------------ > *Lähettäjä:* Ali Kusay <akus8...@uni.sydney.edu.au> > *Lähetetty:* tiistai 25. kesäkuuta 2019 20.52.33 > *Vastaanottaja:* Sarameri, Jesse > *Kopio:* pymol-users@lists.sourceforge.net > *Aihe:* Re: [PyMOL] Export molecule does not keep changes > > > Hi Jesse, > > > > I am not aware of a structure file (i.e. PDB) which can store information > such as color and thus when you load a PDB file pymol applies the default > colors to it. > > > > You can however make it so that all proteins loaded into pymol are > automatically assigned the grey colour, this is done by editing the pymolrc. > > > > In the menu go: > > File -> Edit -> pymolrc (will create file) -> type “set cartoon_color, > grey80” > > > > When you close and reopen pymol, this will ensure that all proteins loaded > into pymol are given the grey80 colour, you can make any additional edits > to the pymolrc file as you please i.e stick color is still default > > > > Cheers, > > > > Ali > > > > *Ali Kusay *| BPharm (Hons) | PhD Candidate & Pharmacist > > *Supervised by *A/Prof Thomas Balle > > The University of Sydney School of Pharmacy | Faculty of Medicine and > Health > > 424, Brain and Mind Centre | The University of Sydney | NSW 2050 > > > > *From: *"Sarameri, Jesse" <jesse.saram...@helsinki.fi> > *Date: *Wednesday, 26 June 2019 at 6:34 pm > *To: *"pymol-users@lists.sourceforge.net" < > pymol-users@lists.sourceforge.net> > *Subject: *[PyMOL] Export molecule does not keep changes > > > > Hello! > > (English is not my native language; please excuse typing errors.) > > Goal is to recolor molecule so it stays that way after the edit. > > > > This is how I thought it would work: > > Lets start by opening any molecule (like downloading 5jh0.cif from > https://www.rcsb.org/structure/5jh0) > > Changed the color of the molecule to grey, save as session (.pse file), > open it and still grey, great! > > But if I want to export to molecule (.pdb for example), open the molecule, > no changes applied. > > Tried to change Saved state settings and different formats but no effect. > > No error messages either. > > > > I did RTFM and STFW not able to find answer. > > (If I missed it, feel free to send pics with red circles and arrows to > highlight it.) > > > > Software and hardware used: > > Open source PyMOL version 2.1.0. > > Windows 10 > > Lenovo X280 Laptop > > > > Many thanks for help incase someone else might encounter this problem. > > > > Regards, > > Jesse Sarameri > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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