Thanks Elaine I tried with a BILD file (option 2) and that works well. Best Hernando -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Thursday, April 11, 2019 12:21 PM To: Hernando J Sosa Cc: chimera-users@cgl.ucsf.edu Mailing List Subject: Re: [Chimera-users] Drawing vectors Hi Hernando, “Best” depends on personal preferences, but there are two main approaches. (1) draw pseudobonds between the two structures. This could be done by listing specifications of the pairs of atoms in a text file (pseudobond file) and reading it in with Pseudobond Reader, <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fpbreader%2Fpbreader.html&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cfdf84225579a4adc615908d6be99c03f%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636905964898957264&sdata=0ei2Lh28LCMLyHyyNUaZaUCHHa7rhXzbyBK6tkvkd30%3D&reserved=0> ...or by writing a command script with distance measurements between all the pairs of atoms. You could hide the distance labels afterward, for example with the Distances tool. <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fdistance.html&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cfdf84225579a4adc615908d6be99c03f%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636905964898957264&sdata=6R39jMPzaQnf5Lo%2BaFOSv0wAoGIInF6OzyiaOI86dDk%3D&reserved=0> <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fstructuremeas%2Fstructuremeas.html%23distances&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cfdf84225579a4adc615908d6be99c03f%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636905964898957264&sdata=YvC65xCvjF7Vma9D01xC3fyqVIvPWenIPK8SorXDmuk%3D&reserved=0> You can control pseudobond line style, line width, color, or change them to sticks in the Selection Inspector or with the “setattr” command. <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Finspection.html&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cfdf84225579a4adc615908d6be99c03f%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636905964898957264&sdata=kbcKBqYSRsH9SBwtp7WVq0YDGeCxxjUcaScUFSjca%2Bw%3D&reserved=0> <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fsetattr.html&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cfdf84225579a4adc615908d6be99c03f%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636905964898957264&sdata=R3aPq5QjWm%2FLBnn%2BeXq95fyH0RQa3%2BAsh3iMtq2ujno%3D&reserved=0> (2) create a simple text file in BILD format describing cylinders or 3D arrows between the pairs of points. Then opening the file (name ending in .bld) shows the objects. <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fbild.html&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cfdf84225579a4adc615908d6be99c03f%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636905964898957264&sdata=bJCew1z3HjRgLim8XTDMqqf1ra1RDe0zmzuWbEpN15M%3D&reserved=0> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 11, 2019, at 8:42 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Dear UCSF-Chimera, What would be the best approach to draw vectors between equivalent atoms of two alternative conformations of a protein. Is there a script available to do this? Thanks Hernando