[PyMOL] Issues when displaying surfaces of two objects in two distinct display grids
Hi altogether, using Pymol open source 2.4, I'm trying to simultaneously display two objects (OB1 & OB2) side-by-side in a grid (>Display>Grid>By object). So I have one object (OB1) on the left part and one (OB2) on the right. Now, in order to have two surfaces on the left covering different areas of the protein, I need to partially duplicate the object on the left (OB1). Both surfaces on the left are shown properly. But if I do the same with the second object (OB2, on the right part of the screen), I run into issues: for none of the objects created as duplicates (copies) from OB2 I am able to display the corresponding surface. For the original object (OB2) it works. But this is not what I want. Does anyone know what's going on and how to circumvent this problem? Many thanks in advance & best wishes, Vedat pEpkey.asc Description: application/pgp-keys ___ 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
Re: [PyMOL] How to print the time stample on each frame of the movie for molecular dynamics trajectory in Pymol?
Hi Yeping,
It's possible to create a such a label, but unfortunately it's a bit
complicated. The following script places a label with 2500 states in the upper
right corner of the display area.
# create a discrete multi-state object with one labeled atom per state
pseudoatom tmp, label=pending
python
for i in range(2500):
cmd.label("tmp", "'{} ps'".format(i * 80))
cmd.create('timestaple', 'tmp', 1, i + 1, discrete=1)
python end
delete tmp
# anchor the label in the upper right corner
set label_screen_point, [1, 1, 0], timestaple
set label_relative_mode, 1, timestaple
# align the label to the bottom left of the anchor
set label_position, [-1, -1, 0], timestaple
Those label settings are documented here:
https://pymol.org/d/setting:label
Hope that helps.
Cheers,
Thomas
> On Jan 15, 2020, at 5:22 AM, sunyeping via PyMOL-users
> wrote:
>
> Dear All,
>
> I load a molecular dynamics (gromacs) trajectory into Pymol and wish to make
> a movie with it. The trajectory contains 2500 frames, corresponding to 200 ns
> simulation time, so each frame represents 80 ps. I wish to print time stample
> on each stample. For example, on the first frame, " 0 ns" is printed; on the
> second frame, "80 ps" is printed; on the third frame, "160 ps" is printed.
> How I cannot find any clue how to do this. Could you have any clue how to
> finish this task?
>
> Best regards,
> Yeping Sun
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] diaplay actural sizes in Pymol
Hi Ting, This will display the assemblies (biological units) in a grid. The result should look like in the attached image. set assembly set all_states set grid_mode fetch 1igt 1s58 3j3i 2ztn 6ui6 5wtf 3iyo, type=mmtf zoom The "assembly" setting replaces the use of type=pdb1. It works with type=cif and type=mmtf. https://pymolwiki.org/index.php/Assembly Hope that helps. Cheers, Thomas > On Jan 20, 2020, at 7:21 AM, Ting Hu via PyMOL-users > wrote: > > Dear Pymol-users support, > > I want to compare the sizes of different virus and IgG in Pymol. But they are > exhibiting similar sizes. how can i change that? > > the commands I enter are as below: > fetch 1igt, type=pdb1 > fetch 1s58, type=pdb1 set all_states, on > fetch 3j3i, type=pdb1 set all_states, on > fetch 2ztn, type=pdb1 set all_states, on > fetch 6ui6, type=pdb1 set all_states, on > fetch 5wtf, type=pdb1 set all_states, on > fetch 3iyo, type=pdb1 set all_states, on > fetch 1s58, type=pdb1 set all_states, on > > Best regrds > Ting > > ___ > 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
