[Chimera-users] Drawing vectors

[Hernando J Sosa]

Thanks Elaine

I tried with a BILD file (option 2) and that works well.

Best

Hernando



-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Thursday, April 11, 2019 12:21 PM
To: Hernando J Sosa
Cc: chimera-users at 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 at 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