<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div dir="ltr">Hello again and thank you for helping.</div><div dir="ltr">I exactly need the formation a covalent bond and because of that i used the Join Model option and although i studied the Building Structure part of manual i coudn't understand that how two atoms, that the bond should be formed between them, are selected.</div><div dir="ltr">Please guide me more.Thanks.</div> <div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"> <div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;"> <div dir="ltr"> <hr size="1"> <font size="2" face="Arial"> <b><span style="font-weight:bold;">From:</span></b> Elaine Meng <meng@cgl.ucsf.edu><br> <b><span style="font-weight: bold;">To:</span></b> A Amiri <atefeh_amiri23@yahoo.com> <br><b><span style="font-weight:
bold;">Cc:</span></b> "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> <br> <b><span style="font-weight: bold;">Sent:</span></b> Tuesday, 30 July 2013, 10:22:22<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [Chimera-users] Hello<br> </font> </div> <div class="y_msg_container"><br><div dir="ltr">Hello,<br></div><div dir="ltr">Join Models is for when you want to combine models AND make a covalent bond between them. <br></div><div dir="ltr"><br></div><div dir="ltr"><<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html</a>><br></div><div dir="ltr"><<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join</a>><br></div><div dir="ltr"><br></div><div
dir="ltr">As explained in the link above, to use Join Models you must select two atoms in different models, each bonded to at most one other atom, to indicate where the bond should be formed, and enter values as needed to specify the geometry of bond formation (see the link for details). The Apply button won't be active until those things are done. (You can also see the manual by clicking the Help button on the dialog.)<br></div><div dir="ltr"><br></div><div dir="ltr">However, if you just want to combine models and don't care about making a bond, you should instead use the "copy/combine" function in the Model Panel. Model Panel is in the menu under Favorites. Then you would have to choose the two models in the left side of the Model Panel to make the copy/combine button on the right side available. Or, you can use the "combine" command that has the same capabilities as the Model Panel function.<br></div><div
dir="ltr"><br></div><div dir="ltr"><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine</a>><br></div><div dir="ltr"><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html</a>><br></div><div dir="ltr"><br></div><div dir="ltr">I hope this helps,<br></div><div dir="ltr">Elaine<br></div><div dir="ltr">----------<br></div><div dir="ltr">Elaine C. Meng, Ph.D. <br></div><div dir="ltr">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br></div><div dir="ltr">Department of Pharmaceutical Chemistry<br></div><div dir="ltr">University of California, San Francisco<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">On Jul 30, 2013, at 5:29 AM, A Amiri <<a ymailto="mailto:atefeh_amiri23@yahoo.com"
href="mailto:atefeh_amiri23@yahoo.com">atefeh_amiri23@yahoo.com</a>> wrote:<br></div><div dir="ltr"><br></div><div dir="ltr">> Hello.<br></div><div dir="ltr">> I have a problem with chimera! I want to combine two different pdb file by chimera , which will be merge into a single model.<br></div><div dir="ltr">> I used the "join models" section from chimera but the "apply" button was inactive and i don't know how i can activate it!<br></div><div dir="ltr">> please help me.<br></div><div dir="ltr">> thank you for your useful software.<br></div><div dir="ltr"><br></div><br><br></div> </div> </div> </div></body></html>