Re: [PyMOL] H bonds

Hi Amali, For adding hydrogens, I have found that PyMOL does an OK job normally, but if you need more accurate placement of hydrogens, I can recommend using Reduce. http://kinemage.biochem.duke.edu/software/reduce.php HTH, Matthew Baumgartner On 11/11/2015 02:06 AM, Osvaldo Martin wrote:

Re: [PyMOL] H bonds

Hi Amali, Aspartic acid is also assumed to be charged (like Arg), but with opposite sign. Acids like Asp release hydrogens, bases like Arg accept hydrogens. That's why in one case there is one hydrogen more that what you are expecting and in the other case there is one hydrogen less. Nothing wrong

Re: [PyMOL] H bonds

Dear Prof. Osvaldo, Arg residue problem is solved. Thank you very much. Other thing is for Aspartic acid the program doesn't add H to the OH group. What is the reason behind this. Thank you. On Wed, Nov 11, 2015 at 11:17 AM, Osvaldo Martin wrote: > Hi Amali, > > By the =NH group do you mean on

Re: [PyMOL] H bonds

Hi Amali, PyMOL has parameters like h_bond_max_angle that are defined in terms of aceptor-donor-hydrogen, hence if hydrogens are not present PyMOL has to guess the position of hydrogens. If you need to add hydrogens you can use PyMOL’s h_add command, alterna

Re: [PyMOL] H-bonds representation

Dear all :) I want to find Hbonds beetween different helices in the membrane receptor ( H bonds beetween sidechains only) I know possible way to do it wihin selection if I defined different helixes but is there any way to find almost all Hbonds between polar sidecains groups ? Could I use find

Re: [PyMOL] H-bonds representation

Thanks Jason. It works quite well in case of not very compliated ligands ( e.g bonds beetween aa-tRNA and the aa-tRNA syntase were correct ) but in the sugar-bound enzyme there were some mistakes in representation of the H-bonds netween water/ligand/active center ( some water also partisipate in

Re: [PyMOL] H-bonds representation

James, > Is there any semi-avtomated way to find ligand binding pocket and do all > such things ? For your given object, click A > preset > ligands sites > cartoon. Try other options under that menu. Cheers, -- Jason > 2011/11/28 Thomas Holder >> >> Hi James, >> >> most trivial manner: >> >>

Re: [PyMOL] H-bonds representation

Thanks, Thomas, Jason both of the methods are useable :) By the way I've forced with the problem of the representation of the active sites of different enzymes. I need to view all my protein as the cartoons and the ligand as the shpere in the ligand binding pocket. Besides I need to mark residues

Re: [PyMOL] H-bonds representation

Hi James, most trivial manner: as cartoon show sticks, resn LEU+ILE+VAL set cartoon_side_chain_helper and eventually something like this: show spheres, resn LEU+ILE+VAL and not name N+O+C set sphere_transparency, 0.5 Cheers, Thomas On 11/28/2011 02:58 PM, James Starlight wrote: > Another

Re: [PyMOL] H-bonds representation

Another question also linked with the non-covalent interaction. In particular I wounder to know how i Could represent all hydrophobic ( Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd like to represent the hydrophobic core of the proteins made from those residues. Thanks,

Re: [PyMOL] H-bonds representation

While the single acceptor H-bond is most common, bifurcated (or three-centred) H-bods are not uncommon in crystal structures, as described starting page 22 of GA Jeffrey's book: http://www.amazon.com/Introduction-Hydrogen-Bonding-Physical-Chemistry/dp/0195095499/ref=sr_1_2?ie=UTF8&qid=1322331503

Re: [PyMOL] H-bonds representation

Thomas, thank you for so detailed explanation. This way works good but I'd like to ask you about possibe Hbonds in the protein chain. As I remember for protein physics courses the H atom is always donor for only ONE H-bond ( and O or N atoms could be akceptors for 1 or 2 Hbonds) But In my case t

Re: [PyMOL] H-bonds representation

Hi James, > As I've understood there are no posible ways to represent H-bonds in > proteins in explicit manner. So I'm looking for possible way to do it > via some plugin or another way. PyMOL can find polar contacts and represent them as dashed lines. You don't need any extra plugin. http://py

Re: [PyMOL] H-bonds and VDW

Kun, When I'm interested in dimer interfaces, or protein ligand contacts I usually use Molprobity to define the interface. http://molprobity.biochem.duke.edu/ It is a bit of a process, but here's the rundown: Load your .pdb into molprobity Add hydrogens Visualize interface contacts Then select

Re: [PyMOL] H-bonds

On Tuesday 06 January 2004 20:06, Sanishvili, Ruslan wrote: > Is there a way to calculate and display H-bonds within a selected model > without going through the distance wizard? Selecting the pairs of atoms > manually via the distance wizard seems very inefficient and even > dangerous (too subject

RE: [PyMOL] H-bonds too thick

> From: Mario Sanchez [mailto:sanc...@if.sc.usp.br] > I am drawing hydrogen bonds using command dist, but the "rayied" image > has a too thick line to these interactions. I was not able to find the > command to set the thickness of it, but I hope someone > (DeLano?) will be > able to help me. Yo