Re: [PyMOL] 2 Molecules superposition

Align menu under plugin: [image: image.png] It has multiple algorithm for alignments. [image: image.png] Regards, Saurabh Gayali -- *Saurabh Gayali* Business Analyst [Excelra], Former Research Scientist [IGIB] saurabh.gay...@gmail.com / +91 8800412916 <h

Re: [PyMOL] Running pymol without launching window in batch

Apart from others' reply, I believe pymol will run .pml files while python will run .py files. Regards, Saurabh Gayali -- *Saurabh Gayali* Business Analyst [Excelra], Former Research Scientist [IGIB] saurabh.gay...@gmail.com / +91 8800412916 <http://exa

Re: [PyMOL] Questions about licenses

I would suggest you to use the PyMol open Source version for Research Publications. https://github.com/schrodinger/pymol-open-source Regards, Saurabh Gayali -- *Saurabh Gayali* Business Analyst [Excelra], Former Research Scientist [IGIB] saurabh.gay...@gmail.com

Re: [PyMOL] File attachments

You can always upload zip to google drive and share link. -- *Saurabh Gayali* Business Analyst [Excelra], Former Research Scientist [IGIB] saurabh.gay...@gmail.com / +91 8800412916 <http://example.com/>Bangalore, India [image: Mailtrack] <https://mai

Re: [PyMOL] separate two molecule as an object from a complex of four molecules

Have you tried this: https://pymolwiki.org/index.php/Split_object -- *Saurabh Gayali* Business Analyst [Excelra], Former Research Scientist [IGIB] saurabh.gay...@gmail.com / +91 8800412916 <http://example.com/>Bangalore, India [image: Mailtrack]

Re: [PyMOL] problem with ray of PNG using pymol in non-gui mode

Have you tried setting ray_trace_mode? Info here: https://pymolwiki.org/index.php/Ray -- *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/>New Delhi, India [image: Mailtrack] <https://mai

Re: [PyMOL] how to create multi-model pdb for protein-ligand complex?

Have you tried the save command after opening both files? https://pymol.org/dokuwiki/doku.php?id=command:save Though not sure how the different poses will merge. Also looking for a solution for a similar problem. -- *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay

Re: [PyMOL] Distorted 3-10 helix

Have you tried the "DSS" command? https://pymolwiki.org/index.php/Dss ------ *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/>New Delhi, India [image: Mailtrack] <https://mailtrack.

Re: [PyMOL] Ruge problem visualization of PDBQT file on pymol

I hope the "show spheres" command represents the ligands better for you. ------ *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/>New Delhi, India [image: Mailtrack] <https://mailtrack.

Re: [PyMOL] Structure alignment -- general question

extra_fit command will work in this scenario. More information in documentation here: https://pymolwiki.org/index.php/Extra_fit -- *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/>New Delhi,

Re: [PyMOL] How to enable Pymol when give ModuleNotFoundError: No module named '_tkinter' error

Have you tried installing tkinter by following command. sudo python -m pip install tk -- *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/>New Delhi, India On Fri, Jun 18, 2021 at 7:23 AM G

Re: [PyMOL] Programmatically adding hydrogen and remove water to multiple PDB files

You should use autodocktools [ADT] or openbabel for this purpose. Converting PDB to PDBQT. -- *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/>New Delhi, India On Thu, Jun 17, 2021 at 4:01 PM G

Re: [PyMOL] Farewell

Thank you for the incredible support to the community via this marvelous tool. Hope to see more of your wonderful work in future. Best Regards, -- *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/&

Re: [PyMOL] [EXTERNAL] png command in Educational Pymol

files where models are saved as frames and I want a particular frame. I dont know the question should be in the same thread or I should start a new one. -- *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.

Re: [PyMOL] Skip Activation Window Remove

You can always use the Educational version of Pymol. Regards, *Saurabh Gayali* - <https://www.avast.com/en-in/recommend?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=de

Re: [PyMOL] Align more than two structures

extra_fit aligns multiple objects to a reference object. https://pymolwiki.org/index.php/Extra_fit Regards, *Saurabh Gayali* - On Wed, Jul 10, 2019 at 9:25 AM Neena Susan Eappen wrote: > Hello PyMOL users, > &g

Re: [PyMOL] How to color stick and surface representation separately

ed to align them] now You can choose any visualization for both moleculaes as they are separate files. Regards, *Saurabh Gayali* - <https://www.avast.com/en-in/recommend?utm_medium=email&utm_source=link&utm_ca

Re: [PyMOL] .

l/ Regards, *Saurabh Gayali* - On Wed, Jul 3, 2019 at 5:50 PM O.L. Simpson wrote: > Dear Pymol Users, > > How can I integrate PyMOL into Jupiter notebooks to visualise structures?

Re: [PyMOL] Export molecule does not keep COLOUR* changes - RESOLVED

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