Thank you, Blaine. Although I already solved it by doing using these two
lines instead of sess.cmd.util.cbac("all"):
sess.cmd.color("atomic", "all", quiet=1)
sess.cmd.color("cyan", "(name C*)", quiet=1)
I will also try your way, anyway :)
Kind regards,
El lun., 14 sept. 2020 a las 19:41, Mooers, Blaine H.M. (HSC) (<
blaine-moo...@ouhsc.edu>) escribió:
> Hi Antonio,
>
> I got the same error message after the second line but this worked for me.
>
> /Applications/PyMOL.app/Contents/bin/python
> >>>from pymol import cmd
> >>>fcmd.fetch("5da6")
> >>>fcmd.do("show sticks; hide cartoon;orient")
> >>>fcmd.util.cbac('all')
> >>>fcmd.png("testcbacSticks.png")
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
> ________________________________________
> From: Antonio Serrano [aserra...@ucam.edu]
> Sent: Monday, September 14, 2020 10:57 AM
> To: pymol mailinglist
> Subject: [EXTERNAL] [PyMOL] Color by Atom from CLI (not PyMol's GUI)
>
> Hi. I'm working with PyMol's Python API from the terminal. I would like to
> color the molecules in my session by atom using the command util.cbac(). I
> want them in cyan because I'm deleting the two molecules involved and
> reopening the files with those molecules several times inside a loop. My
> first attempt was this:
>
> import pymol2
> sess = pymol2.PyMOL()
> sess.start()
> sess.cmd.load("./cyclodextrin_rec.mol2", object = "rec")
> sess.cmd.load("./cyclodextrin_lig.mol2", object = "lig")
> sess.cmd.util.cbac("all")
>
> After that last command, I get the following warning message: "PyMOL not
> running, entering library mode (experimental)". It is supposed to work, but
> I don't get the molecules colored by atom. I also tried with the following
> last command instead of sess.cmd.util.cbac("all"):
>
> import pymol
> pymol.util.cbac("all")
>
> But still doesn't work. Any clue? Thx.
>
> Antonio Serrano
>
> [http://ucam.edu/logo-firma-electronica.png]
> ________________________________
> "Este mensaje es privado y confidencial y se dirige exclusivamente a su
> destinatario. Si usted recibe este mensaje por error, no debe revelar,
> distribuir o copiar este e-mail. Por favor, comuníquelo al remitente y
> borre el mensaje y los archivos adjuntos de su sistema. No hay renuncia a
> la confidencialidad ni a ningún privilegio a causa de una transmisión
> errónea o por mal funcionamiento".
>
> "This message is private and confidential and it is intended exclusively
> for the addressee. If your receive this message by mistake, you should not
> disseminate, distribute or copy this e-mail. Please inform the sender and
> delete the message and attachments from your system. No confidentiality or
> any privilege regarding the information is waived or lost by any
> mistransmission or malfunction".
>
> No me imprimas si no es necesario.
> Don't print me unless it's necessary.
>
>
Antonio Serrano
--
"Este mensaje es privado y confidencial y se dirige exclusivamente a su
destinatario. Si usted recibe este mensaje por error, no debe revelar,
distribuir o copiar este e-mail. Por favor, comuníquelo al remitente y
borre el mensaje y los archivos adjuntos de su sistema. No hay renuncia a
la confidencialidad ni a ningún privilegio a causa de una transmisión
errónea o por mal funcionamiento".
"This message is private and
confidential and it is intended exclusively for the addressee. If your
receive this message by mistake, you should not disseminate, distribute or
copy this e-mail. Please inform the sender and delete the message and
attachments from your system. No confidentiality or any privilege regarding
the information is waived or lost by any mistransmission or malfunction".
No me imprimas si no es necesario.Don't print me unless it's necessary.
_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe:
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
