Hi Blaine, Setting ambient to 0.1 didn't change anything. Setting to 0.4 and higher improves brightness but makes representation not very "esthetically pleasing" - the color is definitively oversaturated.
Thanks, Vitali -----Original Message----- From: Mooers, Blaine H.M. (HSC) <blaine-moo...@ouhsc.edu> Sent: Tuesday, May 26, 2020 6:31 PM To: Stanevich, Vitali [JRDUS] <vstan...@its.jnj.com>; pymol-users@lists.sourceforge.net Subject: [EXTERNAL] RE: volume representation is extremely dark colored WARNING: This email originated from outside the company. Do not click on links unless you recognize the sender and have confidence the content is safe. If you have concerns about this email, send it as an attachment to 'suspiciousem...@its.jnj.com'. Hi Vitali, Maybe ambient was set to a large negative value. Doing so has not impact on line drawings. Try resetting it to the default value. set ambient, 0.1 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: Stanevich, Vitali [JRDUS] via PyMOL-users [pymol-users@lists.sourceforge.net] Sent: Tuesday, May 26, 2020 4:32 PM To: pymol-users@lists.sourceforge.net Subject: [EXTERNAL] [PyMOL] volume representation is extremely dark colored Hello everyone, I have a problem of creating useful volume representations in Pymol version 1.8.6.2<https://urldefense.proofpoint.com/v2/url?u=http-3A__1.8.6.2&d=DwQFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4&s=RPm4waFOpdYkr0DWzikqf33ejGbyEIpp1mroeQkUqjc&e=>. Lines representation behaves as expected, but anything volume related (sticks, surface, cartoon) is drawn as a very dark surface, see example image at the link below: https://www.dropbox.com/s/nc8vqs42ki5l0zs/vs1.png?dl=0<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.dropbox.com_s_nc8vqs42ki5l0zs_vs1.png-3Fdl-3D0&d=DwMFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4&s=Wug1vVUQk8jevkmDUEfqd8P7wnR8KN82kBpEqNiWbE8&e=> Is there setting in Pymol which can bring volume-related representation to something more normal? Or do you think it's non-Pymol problem with drivers compatibility and etc issues? Thanks in advance! Vitali Stanevich, PhD Scientist Janssen R&D _______________________________________________ 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
