[Chimera-users] saving coordinates from a session and re-opening them in another one

Boaz Shaanan bshaanan at exchange.bgu.ac.il
Wed Jul 13 11:35:08 PDT 2011

Hi Elaine,

Thanks a lot for your prompt reply and suggestions. I'll try them soon and report if I still have problems. I did try to edit the saved-pdb file but edited out the secondary structure (sheet, helix) cards rather than the connect cards. Thanks for pointing this out. As for hiding ribbons and showing all atoms: I think I tried something like that but it didn't bring back all the atoms. I'll try again with the new file. Next time I'll use the 'report but' button.

  Thanks again,


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

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: Wednesday, July 13, 2011 8:37 PM
To: בעז שאנן
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] saving coordinates from a session and re-opening them in another one

Hi Boaz,
I believe the saved PDB file includes all the selected and displayed atoms in their correct locations from your session, but the bonds are messed up.   That is a bug and the main problem.

selected and displayed in session: 2 models, 52 residues, 377 atoms, 361 bonds

contents of PDB file: 2 models 52 residues, 377 atoms, 381 bonds (and some of those bonds are wrong)

Also contributing to the confusion is that the default initial display tries to simplify structures to ribbons and does not show all the atoms.  To see all the atoms, hide ribbon, display all atoms/bonds (for example, commands: ~ribb; disp ).

If I simply remove all the CONECT records from the PDB file, it is fine (file no-conect.pdb is attached).  You just need to display all atoms as mentioned above.

It is OK to attach files to a chimera-users message as you did, but usually the better way to report problems to the developers is to use "Help... Report a Bug" in the Chimera menu, which will automatically include information about your computer and what version you are using.  It also allows attaching data and including your email address if you wish a response.

One of will file this problem soon and include you on the notification list.
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 13, 2011, at 8:19 AM, Boaz Shaanan wrote:

> Hi
> I save selected & displayed coordinates (using save pdb) from a session, in order to incorporate them into another session. It’s a selected zone around the active site. When I open them in the new session they look strange. Also, the saved coordinates don’t always contain the full set of displayed coordinates (I’ve done this several times on different structures and it seems particularly but not just on pdb’s with aniso card). I’m attaching the session whose coordinates I saved + the saved coordinates (I hope that’s OK with the BB policy). Please help me figure out the problem.
>     Thanks,
>                   Boaz
> <2ez9_ThDP-MAP_waters.py><2ez9_ThDP-MAP_displayed.pdb>

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