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 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)
>
> then I may use the following command to switch to the state in
> multi_model pdb, which could be important:
> cmd.set('state','5','my_pdb*')
>
> Is it possible to print the number of the state which has
> 1) the maximal number of the hydrogen bonds?
> 2) has a particular hydrogen bond of my interest?
> Cheers,
> Enrico
>
>
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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 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)[,3.0[,0]] >This command is showing all possible distances from the selected > atoms Thanking you, > > yours friendly. > Selvaraj, > > > > - > Here's a new way to find what you're looking for - Yahoo! Answers > Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get > it NOW
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 molecule using Pymol. An attempt to do it through mentioning cutoff distance as 3.0, and mode as 0, failed. Command: distance (selection1),(selection2)[,3.0[,0]] This command is showing all possible distances from the selected atoms Thanking you, yours friendly. Selvaraj, Here's a new way to find what you're looking for - Yahoo! Answers Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
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/pml/hbond.py Credits to the original authors. Regards, Shantanu -- Shantanu Sharma, Graduate Student - Dokholyan Group, Dept of Biochemistry & Biophysics, Univ of North Carolina at Chapel Hill 405 MEJ Bldg CB#7260 Chapel Hill, NC 27599-7260 Ph: (919) 966-3137
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_gap", which control the length and spacing of dashes "dash_width" which controls the pixel thickness of dashes "dash_radius" which controls the radius of dashes when ray-traced. You can use "Edit All..." under the settings menu to inspect and adjust these values. In recent versions of PyMOL, labels can be shown or hidden with hide lables, show labels, Unfortunately, font size is not adjustable because PyMOL currently only has one uniform bitmap font. You currently need to use something like PowerPoint, Photoshop, or Illustrator to add nicer labels onto your images. Cheers, Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D.
