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/2013-September/009142.html>> <https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-July/017021.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 <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>> For future: the recommended address for questions is chimera-users@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@iit.it> Subject: Chimera: Problem with electron density Date: January 14, 2021 at 3:03:55 AM PST To: "meng@cgl.ucsf.edu" <meng@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@NEST Istituto Italiano di Tecnologia Piazza San Silvestro, 12 56127 Pisa, Italy Phone: +39 050 509 495 E-mail: francesco.papi@iit.it <mailto:francesco.papi@iit.it> Skype: francesco.papi.89
Thank you so much, Elaine. Kind Regards, Francesco From: Elaine Meng <meng@cgl.ucsf.edu> Sent: giovedì 14 gennaio 2021 17:28 To: Francesco Papi <Francesco.Papi@iit.it> Cc: Chimera <chimera-users@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@cgl.ucsf.edu<mailto:chimera-users@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@iit.it<mailto:Francesco.Papi@iit.it>> Subject: Chimera: Problem with electron density Date: January 14, 2021 at 3:03:55 AM PST To: "meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>" <meng@cgl.ucsf.edu<mailto:meng@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@NEST Istituto Italiano di Tecnologia Piazza San Silvestro, 12 56127 Pisa, Italy Phone: +39 050 509 495 E-mail: francesco.papi@iit.it<mailto:francesco.papi@iit.it> Skype: francesco.papi.89 [cid:image001.png@01D6EA9D.027E6050]
participants (2)
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Elaine Meng -
Francesco Papi