Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

Hi Annemarie, It's actually quite simple to generate a real membrane around your protein and, e.g., to show the head groups. Do you have a PDB ID for the protein, or are they in-house models? Cheers, Tsjerk On Mon, Feb 1, 2016 at 10:57 PM, Julian Heinrich wrote: > Hi Annemarie, > > Have you t

Re: [PyMOL] loading trajectory file

Can I load the gromacs trajectory files or just the amber trajectory files? On Monday, February 1, 2016 10:17 PM, mohammad r wrote: Hi everybody, How can I load a gromacs trajectory file in PyMOL? Thank you, Mohammad. -

[PyMOL] problem saving very large ray traced pngs

Dear all: I'm ray tracing images from a script with the png command, but am having problems saving images larger than ~ 6000x6000. While I get perfect images at 6000x6000, anything larger writes small, empty files (219kb instead of ~50Mb like expected). Is there some sort of buffer size that needs

Re: [PyMOL] superimposition of 2 ligand molecules

Hi, have a look at the 'align' command: http://pymolwiki.org/index.php/Align Best, Julian On Thu, Jan 28, 2016 at 7:13 AM, leila karami wrote: > Dear pymol users, > > I have 2 ligand molecules having similar backbone. There is little > difference between them. When I load them in pymol, I have

Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

Hi Annemarie, Have you tried the following? cmd.translate([x,y,z], object='membrane') replace x,y,z with your translation vector. Cheers, Julian On Sat, Jan 30, 2016 at 8:33 AM, Honegger Annemarie wrote: > I am trying to show some cell surface receptors and to indicate their > position relati

Re: [PyMOL] drawing trajectory files

Hi Mike, These bonds have bond order zero. Incentive PyMOL 1.8 renders those as dashed lines and sticks. Previous versions of PyMOL had no proper support for zero-order bonds, they did render as solid lines, but had no stick representation. You can set all bond orders to 1 with: PyMOL>valence

[PyMOL] loading trajectory file

Hi everybody, How can I load a gromacs trajectory file in PyMOL? Thank you, Mohammad.-- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Mont

Re: [PyMOL] Testing if a .pml script is run in command line mode

Dear list, Moving a bit further with this, I have been trying to find an easy way to iterate through the list of scene names. Or to get them somehow. I don't seem to be able to find any information about this and thought someone probably already knew. Thanks in advance! Folmer 2016-01-27 14:07

[PyMOL] Fwd: drawing trajectory files

Colleagues, When I load an amber topology file and associated trajectory file, the lines for all heteroatoms are drawn as dashed lines (but bonds to hydrogens drawn as solid lines). I can’t seem to find a flag that would turn this feature off… I’d rather see all bonded atoms connected as solid