Re: [PyMOL] volume representation is extremely dark colored

[Stanevich, V. [JRDUS] <vst...@IT...>]

Thanks Thomas and Akbar! "set precomputed_lighting" did the trick and everything looks normal now.

Vitali



-----Original Message-----
From: Thomas Holder <tho...@sc...> 
Sent: Wednesday, May 27, 2020 2:24 AM
To: Stanevich, Vitali [JRDUS] <vst...@IT...>
Cc: Mooers, Blaine H.M. (HSC) <Bla...@ou...>; pym...@li...
Subject: [EXTERNAL] Re: [PyMOL] volume representation is extremely dark colored

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 <pym...@li...> 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) <Bla...@ou...> 
> Sent: Tuesday, May 26, 2020 6:31 PM
> To: Stanevich, Vitali [JRDUS] <vst...@IT...>; pym...@li...
> 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 'Sus...@IT...'.
> 
> 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 [pym...@li...]
> Sent: Tuesday, May 26, 2020 4:32 PM
> To: pym...@li...
> 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/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.