[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 13:41:32 PDT 2011

Hi Elaine,

Thanks for the extra information and for your help on that issue overall. I'll try all your recommendations  first thing tomorrow.

 Best regards,


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 10:02 PM
To: בעז שאנן
Cc: chimera-users at cgl.ucsf.edu Mailing List
Subject: Re: [Chimera-users] saving coordinates from a session and re-opening them in another one

Hi Boaz,
You're welcome!

I'm pretty sure the PDB file you sent had all the atoms: first I used Selection Inspector to see how many atoms were selected in your session, then I opened the PDB file and selected only its contents, same number of atoms.  Just wanted to reassure you  8-)

Also another thing I forgot to mention is that "displayed" can include things that are not visible because they are off to the side or beyond the front/back clipping planes.  After I opened your PDB I moved the clipping planes to show all of its atoms  (also could be done with the command "focus").

Best regards and sorry about the confusing display!

On Jul 13, 2011, at 11:35 AM, Boaz Shaanan wrote:

> 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

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