[Chimera-users] two questions: link card in pdb and bond commans

[Boaz Shaanan]

Hi Elaine,

Thanks for your reply. As per my questions and your answers:
1) I've learnt that for Chimera  to link atoms, the link card should have the distance, as in the pdb's in the pdb databases. If the distance is missing from the link card (as for example in pdb's generated during crystallographic work and produced by Coot or Refmac), Chimera won't link atoms. I tried it on 2pan fresh from RCSB and on the entry once it has been through Coot. The database entry shows the links between Mg's and phosphates in entry 2pan in all subunits, but not in the entry that went through Coot where the link cards don't have the distance (don't ask me why). 

2) Making bonds by 2-clicks: your suggestion Tools... Structure Editing... Build Structure, the "Adjust Bonds" section works fine as well as the alias that you suggested.

  Thanks a lot for your help.

                  Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710





________________________________________
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Sunday, February 17, 2013 3:30 AM
To: בעז שאנן
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] two questions: link card in pdb and bond commans

Hi Boaz,
(1) Chimera does connect atoms for which there are LINK records, but it may be considered a metal-coordination bond and just get a dashed line pseudobond.  However, there are examples where it is a regular covalent bond.  I was just using build 38277 from Feb 13, but I don't think anything related to this has changed recently.

Example of where it becomes a metal coordination bond:
4HHB.pdb:LINK         NE2 HIS A  87                FE   HEM A 142     1555   1555  2.14

Example of where it is a regular covalent bond:
1HZH.pdb:LINK         O2  MAN H 482                 C1  NAG H 483     1555   1555  1.38

Maybe there is something incorrect about the LINK record.  I don't remember the details of when you would use LINK records as opposed to CONECT or SSBOND, but they are all described at the wwPDB site:
<http://www.wwpdb.org/documentation/format33/v3.3.html>

(2) Maybe I'm misunderstanding the question, but you could use command

alias ^dobond bond sel

... which would make "dobond" appear in an Aliases menu, and this menu entry would work when you have two atoms selected.  Also, there is a corresponding GUI, Tools... Structure Editing... Build Structure, the "Adjust Bonds" section.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 16, 2013, at 12:05 PM, Boaz Shaanan wrote:

> Hi,
> 1) I thought Chimera connects two atoms that are marked as linked by the LINK card in the pdb header, is that not the case? It certainly does not work in build 38218 from 5 February (linux x86-64). I'm not sure whether it's my ignorance or a bug hence I'm sending it to the list.
>
> 2) The 'bond' command (for making a bond between two atoms in the same model) only works in command line? If so, will it be difficult to add it to the pull-downs similar to the distance panel (for 2-clicks lazy people like myself)?
>   Cheers,
>               Boaz