[Chimera-users] NOE derived constraints

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 22 08:27:57 PDT 2019

Hi Francesca,
Chimera does not read CYANA upl files directly.  You would have to change the atom descriptions to Chimera command-line specifiers and then either read them in as pseudobonds or as distance commands.

I’m looking at the upl file description here:

…example starts with
# Upper distance limit
 91 THR  HB     93 GLN  H       5.50
 81 ILE  HB     82 PRO  HA      5.19

(1) to read in as pseudobonds in Chimera, remove the comment at the top, and these atom lines could be something like
:91 at hb :93 at h
:81 at hb :82 at ha 

…or if you have more than one model and/or chain you can also specify those, for example with model #0 chain A: 
#0:91.a at hb #0:93.a at h
#0:81.a at hb #0:82.a at ha

You would read in this plain text file with the Pseudobond Reader tool (in menu under Tools…Depiction).

As shown in the link above, you could also give a color and a label on each line, so you could label with the distance value of the constraint.

(2) if you want to see a label of the current distance in the structure (which might be different than the constraint distance), instead change the file to a distance command file.  This is also plain text with the same pairs of atoms, but you would also put “distance” before each pair and name the file ending with .com or .cmd and open it with the “open” command or menu: File… Open.  The lines would be something like the following, with atom specifiers as needed to specify exactly two atoms:

distance :91 at hb :93 at h
distance #0:81.a at hb #0:82.a at ha


(Finally, you might consider using ChimeraX instead of Chimera since it has more features for looking at pseudobonds, like histograms by length with the “crosslinks “ command.  approaches 1) and 2) above are much the same except 
(a) chain specification is different, e.g.
distance :91 at hb :93 at h
distance #0/a:81 at hb #0/a:82 at ha
(b) there is no option to label the pseudobond with the constraint distance, you can only show current distance using the distance command-file approach instead
(c) the pseudobond file should be named ending in .pb and the command file should be named ending in .cxc)

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 22, 2019, at 4:44 AM, Francesca Cantini <cantini at cerm.unifi.it> wrote:
> Dear all,
> I would like to load the upper limits for the distances (constraints) between pairs of atoms (upl file) into my final of structures family. I would like to ask if this is possible with Chimera program
> best regards
> Francesca Cantini

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