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 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 8:37 PM To: בעז שאנן Cc: chimera-users@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. Best, 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 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>

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