Re: [PyMOL] Pseudoatom for a cavity

Hi Kanika - You can get more information on the wiki: https://pymolwiki.org/index.php/Pseudoatom. To answer your specific questions, to make a pseudoatom between the two terminal Ns of Arg 100 on chain A of myobj: ``` pseudoatom my_ps1, myobj and chain A and resi 100 and name NH1+NH2 ``` and

[PyMOL] New plugin: PyMOLProbity

Dear PyMOL Users, I am pleased to introduce a new plugin called PyMOLProbity which allows a PyMOL user to visualize MolProbity-style structural validation data directly in a PyMOL session. The programs Reduce, Flipkin, and Probe from the well-known

Re: [PyMOL] pymol in pthyon get_wizard() problems

Hi Tim - It seems to me that cmd.get_wizard() needs some argument to be passed to it, because right now that function is returning `None`. This explains the error, which states you're trying to call .set_dep() of a `None` object. Hope that helps. Cheers, Jared On Oct 11, 2016, at 2:48 PM,

Re: [PyMOL] 3D printing

Hi Bob - I also haven't done much of anything with 3D printing myself, but having worked on the COLLADA exporter as one of my POSF fellowship projects, I can share some info about the formats themselves and what data is being included in the output files. > Q: What output file types are

Re: [PyMOL] VRML export

d. From what I can tell, it doesn't seem that any of the atom information gets passed into RayRender. --p On 09/23/2016 12:34 PM, Sampson, Jared M. wrote: Hi Paul - The relevant function used for VRML export is RayRenderVRML2() in layer1/Ray.cpp. Cheers, Jared On Sep 22, 2016, at 11

Re: [PyMOL] VRML export

Hi Paul - The relevant function used for VRML export is RayRenderVRML2() in layer1/Ray.cpp. Cheers, Jared > On Sep 22, 2016, at 11:43 AM, Paul Paukstelis > wrote: > > Greetings, > > I've started playing with 3D printing some ball-and-stick models > (primarily

Re: [PyMOL] Session scene compatibility with MacPymol?

Hi Paul - I'm a little late on this thread, but thought I'd add my 2¢. Probably the easiest way get around this issue (as you realize) is probably to save a 1.7.4.5-compatible PSE file. But, for the adventurous, there is another way: With a small effort (and the willingness to use the

Re: [PyMOL] Pymol spheres/circles

Hi Laura - You can also choose single atom selection mode through the menu: click Mouse > Selection mode > Atoms and then click your alpha carbon atom. However, it can be tricky to hit the right atom if you're only looking at a cartoon representation, so I usually prefer to use the PyMOL

Re: [PyMOL] Active site in Pymol

Hi Farzaneh - Are you looking for something programmatic to use for many different structures, or just analyzing a single structure? With just one structure (or a few) you can do most of this using the GUI by eye. 1. To find the length of each H-bond involving your ligand, (let's say the

Re: [PyMOL] What's wrong with my pymol script?

Hi Dd H - `cmd.set` is the wrong command to use here. (It's for changing settings, not for going through states, although some settings can be applied to only a specific state). Instead, you should use `cmd.frame(i)` to move to that frame (state) number. Note that the `width` and `height`

Re: [PyMOL] Modeling protein-dna complex

Hi soumi - A command-line version of what David said is the following: save new_complex.pdb, protein_selection or dna_selection where `protein_selection` and `dna_selection` include all the atoms you want to have in the final PDB. They could be object names if you have each protein and the

Re: [PyMOL] Scripting in Pymol (+)

Hi James - For the first part, you should use split_states and super or cealign, as in my response to one of your emails last month. https://sourceforge.net/p/pymol/mailman/message/35156097/ Then, once you have aligned all the trajectory structures (let's say they're called traj_01 through

[PyMOL] Resetting PyMOL via API for unit testing

tl;dr: Is there a way to fully stop and restart PyMOL "sessions" using the API to avoid crossover between unit tests? Hi everyone - I'm working on unit testing for a plugin and have been trying to figure out how to test some functionality from within a PyMOL session. I have a partially

Re: [PyMOL] Analysis of docking poses from 2 nmr-ensembles

Hi James - First, it will be useful to split the states. split_states ensemble1 split_states ensemble2 delete ensemble1 delete ensemble2 Then, superimpose all structures onto a reference structure for

Re: [PyMOL] Dynamic reloading of plugin

Hi Martin - I've also experienced this kind of tedium. Depending on the type of extension it is, you could also consider writing tests for your function that can be run by either: a) importing PyMOL commands into a python (.py) script and running e.g. `nosetests` or other unit testing

Re: [PyMOL] on the alignment command

Hi Smith - `Align` takes selections as arguments, so something like the following should work. align protA and chain A+B+C, protB and chain E+F+G You could also use `super` or `cealign` instead of align, although with cealign, you should reverse the order of the arguments to achieve the same

Re: [PyMOL] pymolrc location

It should be a plain text file with no filename extension (i.e. no ".txt") in your home directory, with the full path: /Users/yourusername/.pymolrc You can do this with any text editor (including TextEdit--press Cmd-Shift-T to make it plain text), or, alternatively, the shell command: echo

Re: [PyMOL] The Wiki appears outdated or in error

corporated into SVN and Incentive PyMOL soon. Cheers, Jared -- Jared Sampson Columbia University On Mar 24, 2016, at 2:26 PM, Sampson, Jared M. <jms2...@cumc.columbia.edu<mailto:jms2...@cumc.columbia.edu>> wrote: Hi Jim - When I set geometry_export_mode, 1 in PyMOL, then save m

Re: [PyMOL] The Wiki appears outdated or in error

ipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message. From: Sampson, Jared M. [mailto:jms2

Re: [PyMOL] The Wiki appears outdated or in error

er by reply e-mail and destroy all copies of the original message. From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu] Sent: Tuesday, March 22, 2016 1:40 PM To: jimkress...@kressworks.org<mailto:jimkress...@kressworks.org> Cc: pymol-users <pymol-users@lists.sourceforge.net>

Re: [PyMOL] color an isosurface with a rainbow

Hi H. Adam - Try the http://pymolwiki.org/index.php/Distancetoatom script by Andreas Warnecke and use it to set b (or your own custom property in recent Incentive PyMOL versions) based on the distance from a point. Hope that helps. Cheers, Jared -- Jared Sampson Columbia University On Mar

Re: [PyMOL] The Wiki appears outdated or in error

y e-mail and destroy all copies of the original message. From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu] Sent: Wednesday, March 16, 2016 2:28 PM To: jimkress...@kressworks.org<mailto:jimkress...@kressworks.org> Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] The Wiki a

Re: [PyMOL] The Wiki appears outdated or in error

Hi James - If I remember correctly, PyMOL's IDTF output currently only supports triangles meshes (not cylinders or spheres, e.g.), so unfortunately you're basically limited to surface representations for output directly into that format. As a workaround, you could try saving your scene in

Re: [PyMOL] How to tell from within a script if a plugin is loaded?

responsible for adding Plugin menu entries, not for anything else. 3) Inside your test file, do: from pymol import cmd import pmg_tk.startup.my_plugin # (now cmd.my_func should be available immediately) Hope that helps. Cheers, Thomas On 17 Feb 2016, at 11:32, Sampson, Jar

Re: [PyMOL] How to tell from within a script if a plugin is loaded?

hasattr(cmd, "my_func"): # wait some more Hope it helps, Tsjerk On Feb 16, 2016 20:07, "Sampson, Jared M." <jms2...@cumc.columbia.edu<mailto:jms2...@cumc.columbia.edu>> wrote: To my previous message I should add that it works fine if I do: ``` import pmg_tk.startup

Re: [PyMOL] How to tell from within a script if a plugin is loaded?

ude >"extended" functions, even after the function is loaded. ``` PyMOL>print 'ray' in cmd.kw_list True PyMOL>print 'my_func' in cmd.kw_list False ``` Looking forward to any suggestions. Thanks! Cheers, Jared -- Jared Sampson Columbia University On Feb 16, 2016, at 1:5

[PyMOL] How to tell from within a script if a plugin is loaded?

Hi PyMOLers - Maybe some more experienced users/developers can help me out here. I'm trying to write some automated test scripts for the plugin I'm writing, but the test functions end up running before the plugin is loaded. Is there a way to tell if a plugin has been loaded from within a

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

Hi Annemarie - Fun problem. It looks like cmd.transform_selection() only works with "molecule" type objects, not with CGOs. You could try doing something like what's in the 3rd example in http://www.pymolwiki.org/index.php/Axes, calculating the new object matrix itself by transforming the

Re: [PyMOL] using "bymol" in combination with "within"

Hi Andrew - If you're just looking to expand the selection from atoms in water molecules to entire water molecules, I would actually use `byres` instead of `bymol`. The `bymolecule` selector is apparently dependent on how PyMOL sees the bonds (e.g. try `fetch 3ghe, async=0; select test, bymol

Re: [PyMOL] on axis of the subunit

Hi Smith - I’m not quite sure what you mean by "axis of a subunit." If you mean the principal axis of that selection of atoms, `orient my_selection` will get it aligned along one of the axes. Then you can create pseudoatoms on that axis and create a dash between them with the distance

Re: [PyMOL] on axis of the subunit

-01 00:51:46, "Sampson, Jared M." <jms2...@cumc.columbia.edu<mailto:jms2...@cumc.columbia.edu>> wrote: Hi Smith - I’m not quite sure what you mean by "axis of a subunit." If you mean the principal axis of that selection of atoms, `orient my_selection` will get it

Re: [PyMOL] on async

Hi Smith - I assume you’re referring to something like `fetch 1xyz, async=0`. This means that the PyMOL interpreter should wait until the PDB file is downloaded and loaded before continuing with the next step. Normally, the commands will be issued one immediately after the other and the next