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 Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@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@cgl.ucsf.edu] Sent: Wednesday, July 13, 2011 10:02 PM To: בעז שאנן Cc: chimera-users@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! Elaine 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