Re: [PyMOL] hydrogen-bonds detected in the protein-ligand complexes

Good Question I like to know Too. And about Hydrophobic interaction , Is it possible to show the hydrophobic interactions on pymol too? Em qui., 31 de mar. de 2022 às 06:49, Enrico Martinez < jmsstarli...@gmail.com> escreveu: > Dear Pymol users! > Another question related to the analysis of the m

[PyMOL] hydrogen-bonds detected in the protein-ligand complexes

Dear Pymol users! Another question related to the analysis of the multi-model pdb obtained from protein-ligand docking calculations. I am using pymol to visualise protein-ligand interactions between each pose predicted by docking and protein in my script: preset.ligand_cartoon('my_pdb*',_self=cmd

[PyMOL] PyMOL, hydrogen bonds and PQR files with H-atoms

Dear PyMOL Users, I am writing a python script that utilizes the "cmd.find_pairs" and "cmd.distance" functions of the PyMOL API, in order to identify hydrogen bonds in a PQR file and calculate their properties. Since crystal structures rarely contain hydrogens, PyMOL guesses the position of hydrog

[PyMOL] hydrogen bonds delete

Hi, when I use dist selename, select1, select2, mode=2 which produced one hydroge bond between oxygen of residues with anothe oxygen of phosphate groups. I wonder, Which reason cause dist recognize the O-O forming hydrogen bonds in pymol? Another question, are there some simple ways to just ge

[PyMOL] hydrogen bonds displaying

Hi all, How can I display hydrogen bonds of one protein in pymol just like the "Roving Detail" in Demonstration? Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston

Re: [PyMOL] Hydrogen bonds

Dear Selvaraj, You will find useful resources about hydrogen bonding with PyMOL on: http://www.rubor.de/bioinf/tips_modeling.html#addhbond Regards, Jerome Pansanel Le mercredi 23 août 2006 22:48, selva raj a écrit : > Dear Pymol users, >Would anyone tell me how to draw hydrogen bonds be

Re: [PyMOL] Hydrogen bonds

Take a look at this link: http://www.rubor.de/bioinf/tips_modeling.html#addhbond It contains two simple examples and one python script. On 8/23/06, selva raj wrote: Dear Pymol users, Would anyone tell me how to draw hydrogen bonds between interacting atoms in a crystal structure of small

[PyMOL] Hydrogen bonds

Dear Pymol users, Would anyone tell me how to draw hydrogen bonds between interacting atoms in a crystal structure of small molecule using Pymol. An attempt to do it through mentioning cutoff distance as 3.0, and mode as 0, failed. Command: distance (selection1),(selection2)[,3.

Re: [PyMOL] hydrogen bonds

On Fri, 2006-07-07 at 11:22 -0400, Nalam, Madhavi wrote: > Hello, > How do I draw a hydrogen bond between two atoms in PyMol? Please see: http://www.rubor.de/bioinf/tips_modeling.html http://www.rubor.de/bioinf/pml/hbond1.pml http://www.rubor.de/bioinf/pml/hbond2.pml http://www.rubor.de/bioinf/pm

[PyMOL] hydrogen bonds

Hello, How do I draw a hydrogen bond between two atoms in PyMol? Thanks in advance, Madhavi

[PyMOL] hydrogen bonds

Hi, I am a new PyMOL user and I am impressed indeed by the characteristics of this program! Since I am about preparing a paper, I would like to include some pictures prepared with PyMOL. I have a complex ligand/protein and I would like to show the hydrogen bonds interaction between them. I l

RE: [PyMOL] hydrogen bonds

> From: Daan van Aalten [mailto:d...@davapc1.bioch.dundee.ac.uk] > Is there an option to change the following parameters for > drawing hydrogen > bonds: > - thickness of the lines > - number of dashes > - label (on/off, and fontsize) The settings you need to change are: "dash_length" and "dash_

[PyMOL] hydrogen bonds

Hi Warren Is there an option to change the following parameters for drawing hydrogen bonds: - thickness of the lines - number of dashes - label (on/off, and fontsize) cheers Daan ## Dr. Daan van Aalten