Re: [PyMOL] reproduce special vrml-output

Hi Anke - Try `as surface`, which is the equivalent of `hide everything; show surface`. Hope that helps. Cheers, Jared Sent from my iPhone > On May 19, 2017, at 6:43 AM, Anke Schultz > wrote: > > Hi Thomas, > > thanks for the explanation on adjusting view, it works fine. This leaves > me

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, Tim

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 suppo

Re: [PyMOL] VRML export

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 11:43 AM, Paul Pauksteli

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 nucleic acids). I've worked

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 command

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 comma

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 objec

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` arg

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 D

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 tra

[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 workin

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 easier

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 softwa

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 "se

Re: [PyMOL] The Wiki appears outdated or in error

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

Re: [PyMOL] The Wiki appears outdated or in error

tial 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...@cumc.columbia.edu] Sent:

Re: [PyMOL] The Wiki appears outdated or in error

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 Subject: Re: [PyMOL] The Wiki appears outdated or in error Hi

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 23

Re: [PyMOL] The Wiki appears outdated or in error

troy 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 appears outdated or

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 COLLA

Re: [PyMOL] How to store matrix settings for individual scenes?

e: Yeah, but not my preferred choice. Tried to do this the elegant way, but bumping up against Pymol’s limits unless Thomas has a workaround. From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu] Sent: Monday, March 07, 2016 12:15 PM To: Schubert, Carsten [JRDUS] Cc: pymol-users@lists.source

Re: [PyMOL] How to store matrix settings for individual scenes?

Hi Carsten - I'd probably create new objects and use those for superimposition, rather than moving the originals. That would leave your scenes intact. Cheers, Jared -- Jared Sampson Columbia University On Mar 7, 2016, at 12:10 PM, Schubert, Carsten [JRDUS] mailto:cschu...@its.jnj.com>> wrote

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

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, Jared M. mailto:jms2...@cumc.c

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

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

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

x27;t include >"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 Unive

[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 .pml

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 curr

Re: [PyMOL] iterate names in group

Hi Jordan - Grouped object names use dots to indicate group inheritance ("groupA.obj1"), so maybe try something like this: ``` from pymol import stored stored.group_names = [] group_name = "groupA" for obj in cmd.get_names(): if obj[0:len(group_name)] == group_name: # e

Re: [PyMOL] surface accuracy

Hi "Someone Else" - The `rotate` command (http://pymolwiki.org/index.php/Rotate) actually transforms the atomic coordinates of the object in model space, which I believe are only stored to 3 decimal places (as in PDB files), so there will probably be some slight changes in how the surface is re

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

8:33 PM, Smith Liu mailto:smith_liu...@163.com>> wrote: Thanks Jared, it works. In addition, if by your way I created 2 vectors for 2 different chains, will you please show me how to determine the angle formed by the 2 vectors created? Smith At 2015-12-01 00:51:46, "Samps

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 command

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

Re: [PyMOL] .pdb files and rendering software

Hi again, Joe - Try saving in COLLADA format with `save myfile.dae` (in PyMOL v1.7.3.2 or later). If you're using Blender, you'll need to `set collada_geometry_mode, 1`, because Blender only supports polylists for COLLADA import, and not the more effi

Re: [PyMOL] How does PyMOL create .obj file?

Hi Joe - The coordinate system in the .obj file is in camera space, where (0,0,0) is the center of the viewport, positive x to the right, positive y up, and positive z out of the screen toward the viewer. If you want to correlate them, you would need to transform the model coordinates using th

Re: [PyMOL] How to get TTT matrix in PyMOL 1.7.6?

Hi Paweł - Honestly, if you prefer to use matrices, I'd say just go ahead and use get_object_matrix; I doubt it's going away any time soon. You may want to use this in combination with transform_selection. Also maybe check out Christoph

Re: [PyMOL] secondary structure disappears

I'm posting the following solution on behalf of Thomas Holder (whose sourceforge.net email address is currently down due to SF server issues), to ensure it is added to this thread in the archive: This is due to chain identifier conflict. He's merging 6 models with identic

Re: [PyMOL] how to measure the angle between two protein complexes

Hi Yeping - To calculate such an angle, you will need two vectors, which you can create with some pseudoatoms and the orient command. Before you start, you should create named selections for the ring and

Re: [PyMOL] how to measure the distance of 2 hydrophobic residues

Hi Smith - This won't tell you anything about the hydrophobic interaction itself, but if you want to get the distance between the average positions (like center of mass, but without mass) of two groups of atoms to use as an "approximate" distance between the two residues/sidechains/etc., you ca

Re: [PyMOL] efficiency assigning b-factors

Hi Jordan - I think you're doing it exactly the way I would, given an existing dict containing the values. Note, however, that if you have multiple loaded, or multiple chains with the same residue numbers, you may wish to be more specific with your selection string; your current script will al

Re: [PyMOL] MacPyMOL in command line mode

Hi CY - If you're using the -c flag, you shouldn't need a windowing system at all. The following works for me between a MacBook Air and an iMac, both running 10.9.5, with MacPyMOL 1.7.6.0 installed on the iMac. ### begin shell ### (macbook-air)~ › ssh jared@imac Password: Last login: Fri May 2

[PyMOL] Bug report: cmd.fab() with existing object name produces unexpected results and downstream segfault

In the process of investigating Ben Bobay's question about keyboard shortcuts for adding a methyl group, I may have found a bug, or at least unexpected behavior, in cmd.fab(). When first creating a peptide, it works fine: fab ,

Re: [PyMOL] Add fragment

Hi Ben - Try this: editor.attach_fragment("pk1", "methane", 1, 0) Here's how I tracked this down, not having known about this function before your email. cmd._alt() and likewise cmd._ctrl() are functions (you can see for yourself in the source code in pymol/modules/pymol/cmd.py), and they are

Re: [PyMOL] Load very similar molecules into distinct objects?

Hi Jorge - As long as the filenames are different, the molecules should end up in separate objects. If the filenames are in fact the same (e.g. same filename but in different folders), try explicitly naming the objects using the PyMOL command line: load path/to/the/first/mol1.pdb, first_mol lo

Re: [PyMOL] moving objects

Hi Marcelo - Is Object 2 actually a pseudoatom? Or, if not, can it be placed separately from Object 1? If either of those are the case, it would be much easier to place the pseudoatom at a point equidistant from the two ends of Object 1 than mess with rotation matrices, etc. Here’s what I wo

Re: [PyMOL] MacPyMol working dir

Hi Luigi - To get the right working directory, you can use the full path to the binary followed by the `-d` flag to run a command (`cd $PWD`) once PyMOL opens. Personally, I'd alias it in ~/.profile like this: alias macpymol='/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -d "cd $PWD"' Al

Re: [PyMOL] cartoon putty present in pymol

Hi Wenfu - Cartoon putty representation varies the diameter of the putty tube based on the B-factor column in the loaded PDB file. In your example file, all the B-factors are 0.00. Perhaps you could use `cartoon tube` instead, which is similar to putty, but uses a single cartoon_tube_radius s

Re: [PyMOL] Pymol molecular visualisation

Hi James - Here is how I would label your objects in grid_mode: # For each object, create a pseudoatom at its center of geometry to position the label pseudoatom myobj_label, myobj # Set the label text for the pseudoatom label myobj_label, "My Object" # To show the label and the object in the

Re: [PyMOL] Colouring nucleic acids, without changing the colouring of amino acids

Hi Brenton - To avoid coloring e.g. Glycine when you only want to color e.g. guanine, prefix the residue name with “D” (as the residues are shown in the Sequence viewer) for DNA. I believe RNA works the same way with “R” as well. set cartoon_color, green, resn DG To color the DNA backbone, yo

Re: [PyMOL] Chain Selection doesn't work (MacPymolEdu)

Hi Simon - It looks like your default Python is now 3.x rather than 2.x. The built-in function reduce() was moved to functools.reduce() as of version 3.0. You can confirm whether this is the case via “python --version” on the command line. One solution might be to make 2.7 the default again,

Re: [PyMOL] unable to export obj

Hi Albert - Surface mode 2 outlines the mesh edges with thin cylinders, but if I remember correctly, I think PyMOL’s OBJ export doesn’t do cylinders (or spheres or cones), only triangle meshes. You could try exporting to VRML2 (.wrl) or COLLADA (.dae) format and using something like, e.g. Blen

Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

8 objects. > > So it seems okay. But however when I raytrace, I still get all reflections. > When I subsequently type > set spec_reflect, 0 > and then raytrace, the reflections are really turned off. > > Could this be a bug, or do I forget something? > > Thanks > >

Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

Hi Floris - Tsjerk is correct. You can set spec_reflect for a selection. Something like: set spec_reflect, 0, all and not organic This would turn of specular reflection on anything that’s not a “ligand” atom. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://

Re: [PyMOL] Dot representation

Hi Yarrow - 1. Yes, according to the wiki, the dots are located on the vdW surface unless the `dot_solvent` setting is turned on (in which case they’re on the solvent accessible surface). 2. Based on the settings listed with “dot” in their names, it does

Re: [PyMOL] selection of a set of amino acids

Hi Alireza - For renumbering a chain, the program PDBSET in the CCP4 suite is my tool of choice. If your protein is chain A, the command would look something like this: pdbset xyzin my_protein.pdb xyzout my_protein_renumbered.pdb

Re: [PyMOL] homebrew pymol

Hi Ryan - Have a look at this post, which may also help you in creating an app out of your Homebrewed PyMOL. I’d recommend using a symlink within the app bundle to /usr/local/bin/pymol, so when you update with homebrew, you don’t have to ch

Re: [PyMOL] Super, algorithm

Hi Spencer - If you need a superposition algorithm with a published reference, try CEAlign. Some references are listed on the page for the former CEAlign Plugin from before it was incorp

Re: [PyMOL] View Matrix operation

Hi Louris - If your view is centered on the atom from which you would like to draw the line, and oriented the way you want it, you can achieve something similar to what it sounds like you want with the following commands. center myAtom move x, -4 # `move` works in camera space pseudoa

Re: [PyMOL] Access API without the GUI

Hi Doug - You can launch PyMOL with the -c flag for command line only (no GUI). See http://www.pymolwiki.org/index.php/Command_Line_Options for more details. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Nov 11, 2014, at 2:56 PM,

Re: [PyMOL] ligand binding site visualisation

Hi James - You could put in a feature request to ask that non-canonical residues be included in the preset. In the meantime, the Property Selectors, Single-Word Selectors

Re: [PyMOL] How to calculate Hinge angle

Hi Shoeib - It’s hard to say exactly what you need, because it will vary depending on your specific case. If you’re looking for the change in a hinge angle between two structures of multi-domain proteins A and B, you can first superimpose domain 1 of B to domain 1 of A, get the matrix of B, su

Re: [PyMOL] PyMOLWiki Update

Hi Justin - I see this same “weirdness" using the https protocol. If you remove the ’s’ from ‘https’ in your URL, however, it will load properly. It must be on a shared server that has something goofy happening with the handling of https traffic. I think Jason is still the admin for the wiki

Re: [PyMOL] Show all residues forming H-bonds

Jared, I'm a newbie to pythom/PyMOL; how do I get this to work in a pml script? A pointer to an example script would be enough . Thanks Markus From: Sampson, Jared [mailto:jared.samp...@nyumc.org] Sent: Friday, October 10, 2014 4:17 PM To: Markus Heller Cc: pymol-users@lists.sourcefo

Re: [PyMOL] colour surface meshes

Hi David - Yes, indeed, PyMOL can save VRML2 (.wrl) files, although it outputs vertex colors rather than face colors. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Oct 13, 2014, at 11:18 AM, David Pattinson mailto:dj...@cam.ac.uk

Re: [PyMOL] Show all residues forming H-bonds

:10 PM, Sampson, Jared mailto:jared.samp...@nyumc.org>> wrote: Hi Markus - Ah, sorry, I misunderstood your request at first. What about the “acceptors” and “donors” selectors? http://www.pymolwiki.org/index.php/Single-word_Selectors e.g. select hbond_residues, byres ((acceptors within

Re: [PyMOL] Show all residues forming H-bonds

es* as dashes, but not the actual residues. I don’t want the dashes, but I want the residues (i.e. the donors and acceptors) in selectable objects. I hope it’s clearer now what I’m after … Cheers M From: Sampson, Jared [mailto:jared.samp...@nyumc.org] Sent: Friday, October 10, 2014 3:33 PM To:

Re: [PyMOL] measure angles in programming

Hi Lei - The `get_angle` command needs an atom selection for your “tunnel" atoms, which, like the B-factor as Matt mentioned, you can also get using `iterate`: ### # create a list stored.centers = [] # get the macro selection string for each atom in tunnel cmd.iterate("tunnel", 'stored.centers

Re: [PyMOL] Access to pymol commands from the terminal

tarlight mailto:jmsstarli...@gmail.com>>: Hi Jared, many thanks for the suggestion! your method works perfect (i only slightly modified dir for input file) 2014-09-19 20:19 GMT+02:00 Sampson, Jared mailto:jared.samp...@nyumc.org>>: Hi James - I don’t have any experience with Pro

Re: [PyMOL] Access to pymol commands from the terminal

Hi James - I don’t have any experience with Profit. However, instead of using "something like” PyMOL’s `super` command as you asked, you could actually use `super` in your shell session by launching PyMOL in command line mode. Of course

Re: [PyMOL] Access to pymol commands from the terminal

Hi James - What version of PyMOL are you using? For me, using Open Source PyMOL 1.7.2.0, a typical PDB file I tested ends up with more information in that column, not less, after saving from PyMOL: Before: ATOM 1312 NH1 ARG A 198 0.544 14.093 19.655 1.00 34.61 N After: A

Re: [PyMOL] Residue-residue contacts from PDB

Hi Bhumika - Have a look at the CCP4 program NCONT: http://www.ccp4.ac.uk/html/ncont.html. You can run it within the CCP4 GUI or from the command line. For example, for contacts between helices 1 and 2, type these lines at the prompt (or copy and paste), substituting the correct path to the PD

Re: [PyMOL] re： cartoon and line representation

iences -- 发件人：Sampson, Jared mailto:jared.samp...@nyumc.org>> 发送时间：2014年9月2日(星期二) 22:23 收件人：孙业平 mailto:sunyep...@aliyun.com>> 抄　送：pymol-users mailto:pymol-users@lists.sourceforge.net>> 主　题：Re: [PyMOL] cartoon and line representation Hi Yeping - I’m unable to repro

Re: [PyMOL] cartoon and line representation

Hi Yeping - I’m unable to reproduce the behavior you’re seeing—using your commands in Open Source PyMOL 1.7.2.0, I get the whole capsid displayed properly as a cartoon. What version of PyMOL are you using? You could also try using the `all_states` setting instead: fetch 3j2v, type=pdb1, async

Re: [PyMOL] Other coloring strategies based on user-provided properties

Hi Chen - As you guessed, this is commonly done by modifying the B-factor column directly. You can do this with data available to you in PyMOL (e.g. distances, charges, and so forth) using alter and iterate and a fe

Re: [PyMOL] Show cation-pi/pi-pi interactions

Hi Markus - It’s already possible to highlight polar interactions using the `distance` command with mode=2. http://www.pymolwiki.org/index.php/Distance For pi-cation stacking, it might be useful to create pseudo atoms at the average position of the atoms in each charged group or ring in questi

Re: [PyMOL] RMSD for selected residues

Hi Nidhi - The “Align” feature in the GUI uses PyMOL's `align` command, which performs a sequence alignment to use as the basis for structural alignment. It only uses those residues which match exactly, which can throw off the RMSD. Try using `super` or `cealign` instead, which are structural

Re: [PyMOL] Problems with superposing small molecules and transformation

Hi German - I’m not sure I follow exactly what you’re asking, but `align` does its superimposition based on sequence alignment, which isn’t really meaningful for small molecule ligands. I would suggest using `fit`, `super`, or `cealign` instead, which all use just the coordinates, although it’

Re: [PyMOL] How to show the surface border of a specific residue?

Hi Ooker - As I understand it, you want to overlay a line to show which part of the surface belongs to which residue. There is currently no way to do this directly within PyMOL. However, is possible to achieve something similar using multiple layers in a composite image. See this previous th

Re: [PyMOL] Faster installation of plugins during development

Hi Matt - Does your plugin require a GUI, or can you rely on scripted commands and output files for your tests? For any tests that don’t need the GUI, you might consider running them with something like `pymol -ckq my_test.pml`. http://www.pymolwiki.org/index.php/Command_Line_Options Cheers,

Re: [PyMOL] Faster installation of plugins during development

Hi Matt - Does your plugin require a GUI, or can you rely on scripted commands and output files for your tests? For any tests that don’t need the GUI, you might consider running them with something like `pymol -ckq my_test.pml`. http://www.pymolwiki.org/index.php/Command_Line_Options Cheers,

Re: [PyMOL] FW： RE： what is the pymol representation in this figure?

Hi Yeping - I followed Jared's instruction and then show surface, but the surface is still an incomplete plane, unlike what I wish as in the sample. You will probably have to create new objects for those individual residues to show their surfaces in whole. Otherwise, you only get the portion

Re: [PyMOL] what is the pymol representation in this figure?

Hi Yeping - Looks like the following settings are in play here: # different cartoon modes cartoon automatic, alpha1 # for the alpha1 helix cartoon tube, chain P # for the orange, green and blue peptides # hide backbone sticks/lines where cartoon is shown set cartoon_side_chain_helper, on # s

Re: [PyMOL] paste pictures

Hi Yeping - The best way is to upload your image to a file sharing website (e.g. Dropbox, Box, Google Drive, etc.) and include a link to the image (or folder of images) in your message. That way, people only have to download the image if they want to do so. It is also possible to send attache

Re: [PyMOL] command question RE printing out distances to text file

Hi Suzanne - The reason you have been getting only one distance in your output file is that your script is opening the file in “write” mode: f=open('distnew.txt','w') This will overwrite the contents of distnew.txt each time the script is run. If you want to keep all the distances without chan

Re: [PyMOL] filled rings

Hi H. Adam - Try the cartoon_ring_color setting. You can do this per-selection as well. set cartoon_ring_color, blue, my_selection Hope that helps! Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jun 16, 2014, at 4:57 PM, H. Adam

Re: [PyMOL] Visualize Sheets from C-alpha Only Structure

Hi Sean - By “radially symmetric” I mean that a particular representation (e.g. anything in cartoon tube or putty modes, or loops in automatic mode) is drawn as a series of truncated cylinders or cones, so for PyMOL to draw them, basically all it needs for each short section are two end points

Re: [PyMOL] Visualize Sheets from C-alpha Only Structure

Hi Sean - I can confirm this behavior, but I’m not sure it’s unintentional on PyMOL’s part. Rather, I think it may have something to do with two facts: 1) unlike loops, sheets represented in automatic mode are not radially symmetric; and 2) unlike helices, the orientation of the sheet at a par

Re: [PyMOL] align or pair_fit display problem

Hi I-Ji - You say the superimposed atoms are still there; that seems like normal behavior to me. If you disable one of the objects, can you see the other one, and vice versa? If the two structures are nearly identical, you may not be able to differentiate them visually after alignment. If th

Re: [PyMOL] how to count all the Polar contacts

Hi Merlin - Try limiting the distances shown to those between atoms in specific selections using the `distance` command. For example, to show H-bonds to solvent, disable the “my_obj_pol_conts” object created by the technical preset and use the command: distance my_dist, my_obj and not solvent

Re: [PyMOL] Ray trace mode 1 outline thickness

Hi Martin - Try increasing the `ray_trace_gain` setting. Default value is 0.12, so maybe try 1 or 2. If you go much higher, you’ll start to see additional lines or spots. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On May 14, 20

Re: [PyMOL] using a pseudoatom for distance measurement

fer to a real coordinate in the file and it can take any of the twenty models, but when it knows which model to take, it is more probable to work because it refers to the right coordinates. Any comments on that? Cheers Mary On Mon, May 5, 2014 at 4:17 PM, Sampson, Jared mailto:jared.samp...@n

Re: [PyMOL] using a pseudoatom for distance measurement

Hi Mary - There are a couple problems here. First, you’re giving the pseudoatom command a positional argument out-of-order (and after keyword parameters). Keyword parameters can appear in any order, but only if you use the keyword. Otherwise, you must list them in the order specified by the

Re: [PyMOL] Pymol wrl output

g in particular anywhere you see a negative color value? Thanks, Jared -- Jared Sampson Xiangpeng Kong Lab NYU School of Medicine kong.med.nyu.edu ________ From: Grateful Frog [gratefulf...@gmail.com] Sent: Saturday, May 03, 2014 1:53 PM To: Sampson, Jared Cc: Marcelo Marcet;

Re: [PyMOL] Pymol wrl output

Hi Bob - The reason you're getting these errors is because having negative values in a color tuple is not meaningful (you can't have a negative amount of color), and results in undefined behavior. RGB colors use a number in the range 0.0-1.0 (inclusive) for each value in the tuple. What color

Re: [PyMOL] RE： gradually changed colors with b-factor colum

stion is the same with above: how could I correctly label the bar according my data set? Best regards, Yeping ------ 发件人：Sampson, Jared mailto:jared.samp...@nyumc.org>> 发送时间：2014年4月29日(星期二) 04:36 收件人：孙业平 mailto:sunyep...@aliy

Re: [PyMOL] gradually changed colors with b-factor colum

Hi Yeping - I was about to suggest Sean Law’s new spectrumbar script, but I see he beat me to it. You’ll have to adjust the positioning of the bar with some trial and error. Also, in case you get a “NameError: global name 're' is not defined” error

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