Hi Vitali, Try this:
set precomputed_lighting Or upgrade to the latest PyMOL version which has this setting by default. It's an Intel Graphics driver issue, you can read about it in this bug report: https://github.com/schrodinger/pymol-open-source/issues/15 Cheers, Thomas > On May 27, 2020, at 4:26 AM, Stanevich, Vitali [JRDUS] via PyMOL-users > <pymol-users@lists.sourceforge.net> wrote: > > 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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. _______________________________________________ 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
