[Chimera-users] Problem with electron density

[Francesco Papi]

Thank you so much, Elaine.

Kind Regards,

Francesco

From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: giovedì 14 gennaio 2021 17:28
To: Francesco Papi <Francesco.Papi at iit.it>
Cc: Chimera <chimera-users at cgl.ucsf.edu>
Subject: Problem with electron density

Dear Francesco,
Probably you just need to use "vop cover" as described in these previous posts:

<https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009142.html>
<https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-July/017021.html>

Details on the "vop cover" command:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>

For future: the recommended address for questions is chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> (CC'd on this message) ... since I'm not the expert in everything (or might be sick or away from work), it's helpful if more people see the question!

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

From: Francesco Papi <Francesco.Papi at iit.it<mailto:Francesco.Papi at iit.it>>
Subject: Chimera: Problem with electron density
Date: January 14, 2021 at 3:03:55 AM PST
To: "meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>" <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>>

Dear Elaine,
I am using Chimera to get a picture of a small molecule (cif file) in an electron density map (xplor file). My issue deals with the position of some atoms of the molecule in an adjacent unit cell (see attached image) which prevents me to see some atoms within the map. I thought to simply expand the map beyond the cell boundaries and eventually crop the map, but it didn’t work. I have checked different tutorials and the chimera mailing list for troubleshooting but I haven’t found a solution to this problem. Is there something you can think of?
Thank you.
Regards,
Francesco Papi

Francesco Papi, PhD
PostDoc
Center for Nanotechnology Innovation at NEST
Istituto Italiano di Tecnologia
Piazza San Silvestro, 12
56127 Pisa, Italy
Phone: +39 050 509 495
E-mail: francesco.papi at iit.it<mailto:francesco.papi at iit.it>
Skype: francesco.papi.89

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