[PyMOL] Surface not including methyl-lysine

> > Message: 4 > Date: Wed, 24 May 2017 16:45:23 +0800 (GMT+08:00) > From: ??? > Subject: [PyMOL] show surface on pymol > To: pymol-users@lists.sourceforge.net > Message-ID: > <1c6ade2.11d04.15c39a1cba6.coremail.liuyanc...@sibcb.ac.cn> > Content-Type: text/plain; charset="gbk" > > > Dear

Re: [PyMOL] Why does Pymol display the chain as disconnected?

Because in PDB file 1ax8.pdb, residues 25 to 38 are missing. Presumably, this loop was disordered in the crystal and therefore not visible. Annemarie Honegger > On 20 Jun 2017, at 12:10, pymol-users-requ...@lists.sourceforge.net wrote: > > Send PyMOL-users mailing list submissions to > p

[PyMOL] Copy object distorts cartoon backbone

Dear Jordan Comparing the two images, it looks to me that they differ in the cartoon loop settings applied to produce the cartoon: https://pymolwiki.org/index.php/Cartoon_smooth_loops , as well as the helix representation and cartoon highlig

[PyMOL] broken cartoon

Hi Frequently such problems arise because the resulting models a) do not have the residues in their proper order (the patched-in piece gets added to the end of the pdb file) This is particularely severe in DNA, where you have to place b) residue and chain labels do not match (duplicate labels) c

Re: [PyMOL] PyMOL-users Digest, Vol 150, Issue 13

> > Today's Topics: > > 1. how to make selected residues blurry? (sunyeping) > > > -- > > Message: 1 > Date: Fri, 30 Nov 2018 12:14:21 +0800 > From: "sunyeping" > To: "pymol-users" > Subject: [PyMOL] how to make selected r

Re: [PyMOL] PyMOL-users Digest, Vol 152, Issue 3

> > Message: 1 > Date: Thu, 17 Jan 2019 09:53:34 -0300 > From: Clarisa Alvarez > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] PyMOL-users Digest, Vol 152, Issue 2 > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hello > How i could set in pymol to see electr

Re: [PyMOL] Ray tracing after morphing

1. Ray tracing after morphing (Pascal Egea) Which version of PyMOL are you using? In the free edu version, Raytracing is suppressed. In the incentive version, you find under the movie menu the option “ray trace frames” which you need to check. You may also want to first set your viewport (htt

Re: [PyMOL] selecting a plane (perpendicular to zaxis)

You can select by cordinates, e.g. select my_selection, z>12.5 (see https://pymolwiki.org/index.php/Selection_Algebra) So you can select for a range of z-coordinates: select my_selection, z >12.5 and z< 15 best regards Annemarie Dr.

Re: [PyMOL] PyMOL-users Digest, Vol 157, Issue 2

Dear Hao In PyMOL bonds are essentially drawn based on a distance cut-off: Two atoms are considered bonded if distance <= connect_cutoff + (vdw1 + vdw2)/2 You can generally adjust the sensitivity of bond recognition by adjusting the connect_cutoff global variable ( https://pymolwiki.org/index.

[PyMOL] colored secondary structure of two chains with different colors

Dear Stéphane, by default, the cartoon representation takes its color from the color of the c-alpha atoms of your protein. However, you can override this default and assign a specific color to the cartoon representation of a given selection by: set cartoon_color, color, (selection) e.g. set

Re: [PyMOL] PyMOL-users Digest, Vol 158, Issue 6

Dear Yeping You can color the surface independent of the atom color with the command set surface_color, (color), (selection) similarly, you color the cartoon representation dependent of the atom color with the command set cartoon_color, (color), (selection) best regards Annemarie __

Re: [PyMOL] PyMOL-users Digest, Vol 158, Issue 13

Dear sunyeping The critical step in calculating a 3D superposition is the decision of which atom in one structure to fit on which atom in the second structure. Actually fitting the transformation matrix is trivial in comparison. In PyMOL you have different ways to determine what you fit: If you

[PyMOL] amino acids displayed for mutagenesis. Hyp? PTMs? (Bruce Onisko)

Dear Bruce Try the SwissSidechain PyMOL plugin and database https://www.swisssidechain.ch/visualization/pymol.php Annemarie Dr. Annemarie Honegger Dept. of Biochemistry Zürich University Winterthurerstrasse 190 8057 Zürich Switzerland

Re: [PyMOL] PyMOL-users Digest, How to download and install (Pedro Lacerda)

Hi Pedro For Windows, you can get precompiled open source PyMOL from http://www.lfd.uci.edu/~gohlke/pythonlibs/. Dr. Annemarie Honegger Dept. of Biochemistry Zürich University Winterthurerstrasse 190 8057 Zürich Switzerland e-mail:

Re: [PyMOL] PyMOL-users Digest, Vol 185, Issue 11

> -- > > Message: 1 > Date: Sun, 24 Oct 2021 12:32:19 + > From: Xiao Yin Lee > To: "pymol-users@lists.sourceforge.net" > > Subject: [PyMOL] show cartoon mode failed > Message-ID: <1635078740242.19...@kuleuven.be> > Con

[PyMOL] 1. How to label atom at proper positions? (sunyeping)

You can shift the label position relative to the atom position using the “set label_position” command, or, in edit mode, ctrl-shift-left_click to move the labels in the z-direction. See https://pymolwiki.org/index.php/Label for details Annemarie Honegger > > Message: 1 > Date: Tue, 18 Jan 2022