[Chimera-users] finding only ligand-receptor Hbonds instead of all

[Kenward Vaughan]

On 07/09/2018 02:20 AM, Rajlakshmi Chetty wrote:
> Dear Dr Elaine C. Meng,
> 
> Greetings for the day!!
> First of all thank you for your prompt reply.Your specified instructions 
> and answer solved my problem...I am happy for it☺!!!
> My heartfelt thanks to you and and the UCSF Chimera team for  
> consideration and help .
> 

Hi Rajlakshmi,

As a chemist, I would add that you should not exclude water molecules as 
part of your search for ligand-receptor interactions.  While X-ray files 
don't fully represent the state of the system in solution, waters do 
stick around, and there are times when they act as bridges between 
receptor and ligand functional groups (as well as other aspects of 
receptor functioning), both in the solid and solution states.

Be sure to check for these in your interaction search (don't hide or 
delete the waters until you know they are irrelevant)...


Kenward


> 
> Kind regards
> *Kind Regards*
> *Rajlakshmi Chetty*
> Doctoral Student
> School of Chemical Sciences
> Central University of Gujarat
> Gandhinagar 382030 India
> 
> Mobile No :-_ +91 9427178591_
>                      +91 8780155455
> e_mail      :- /rajlakshmi at cug.ac.in <mailto:rajlakshmi at cug.ac.in>/
> _www.researchgate.net/profile/Chetty_Rajlakshmi 
> <http://www.researchgate.net/profile/Chetty_Rajlakshmi>_
> 
> 
> On Sun, Jul 8, 2018 at 10:26 PM, Elaine Meng <meng at cgl.ucsf.edu 
> <mailto:meng at cgl.ucsf.edu>> wrote:
> 
>     Dear Rajlakshmi Chetty,
>     To limit which H-bonds you are finding, first “select” some atoms
>     like the ligand only, and then use the “Only find H-bonds...” option
>     as shown in the dialog.  You have the option turned on, but you
>     probably didn’t select any atoms first.  For explanation of that
>     option and its further options, click the Help button on the dialog
>     or see the same information here at our website:
>     <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html
>     <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>>
> 
>     See also the “If endpoint hidden, show endpoint residue” option.
> 
>     Selected atoms are shown with green outline.  There are many ways to
>     select, such as  Ctrl-click on one ligand atom and then press
>     keyboard up arrow to increase to all ligand atoms, or with a
>     command, etc. as explained here:
>     <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html
>     <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>>
> 
>     I hope this helps,
>     Elaine
>     -----
>     Elaine C. Meng, Ph.D.
>     UCSF Chimera(X) team
>     Department of Pharmaceutical Chemistry
>     University of California, San Francisco
> 
>      > On Jul 7, 2018, at 12:15 AM, Rajlakshmi Chetty
>     <rrlchetty2013 at gmail.com <mailto:rrlchetty2013 at gmail.com>> wrote:
>      >
>      > Dear Sir/Madam
>      >
>      > Greetings for the day!!
>      >
>      > Myself Rajlakshmi Chetty, is Doctoral student in field of
>     Nanomaterials. I am self learning and using chimera since back few
>     days with the help of website tutorials and am stuck with a problem
>     which is described below:
>      >
>      > I have .pdb file format of docked complex (Hex software) in which
>     their is H bond is missing between ligand and receptor when opened
>     in chimera. I tried Tools>structure depiction>find H bond but in
>     that parameters query when i apply I am getting H bond of the whole
>     complex which I don't want. I want to visualize H bond or any
>     bonding between ligand and receptor. Is their any other way or what
>     parameters change i need to do?
>      >
>      > I have attached H bond parameters dialog box with this mail.
>      >
>      > This problem where I am stuck is need for the time for my
>     research work. So your kind help will be a great blessings for me.
>     Your help of gratitude will be highly appreciated.
>      >
>      > Thanking you and looking forward for your reply!!
> 
> 
> 
> 
> -- 
> *Kind Regards*
> *Rajlakshmi Chetty*
> Doctoral Student
> School of Chemical Sciences
> Central University of Gujarat
> Gandhinagar 382030 India
> 
> Mobile No :- _ +91 9427178591_
>                      +91 8780155455
> e_mail      :- /rajlakshmi at cug.ac.in <mailto:rajlakshmi at cug.ac.in>/
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 


-- 
In a completely rational society, the best of us would aspire to be
_teachers_ and the rest of us would have to settle for something less,
because passing civilization along from one generation to the next
ought to be the highest honor and the highest responsibility anyone
could have.     - Lee Iacocca