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

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

Re: [PyMOL] .pdb files and rendering software

Hi again, Joe - Try saving in COLLADAhttp://www.pymolwiki.org/index.php/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

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

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_selectionhttp://www.pymolwiki.org/index.php/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.nethttp://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

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 can

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 pseudoatomshttp://www.pymolwiki.org/index.php/Pseudoatom and the orienthttp://www.pymolwiki.org/index.php/Orient command. Before you start, you should create named selections for the ring and

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

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

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

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

In the process of investigating Ben Bobay's questionhttps://sourceforge.net/p/pymol/mailman/message/34128680/ 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] 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

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

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'

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

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,

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.

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

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 Floris On 09-01-15 16:55, Sampson, Jared wrote: set

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

Re: [PyMOL] Dot representation

Hi Yarrow - 1. Yes, according to the wikihttp://www.pymolwiki.org/index.php/Dots, 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

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 EOF renum 1 chain A EOF To remove the extraneous stuff within

Re: [PyMOL] homebrew pymol

Hi Ryan - Have a look at this posthttps://mathiasbynens.be/notes/shell-script-mac-apps, 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

Re: [PyMOL] Super, algorithm

Hi Spencer - If you need a superposition algorithm with a published reference, try CEAlignhttp://www.pymolwiki.org/index.php/Cealign. Some references are listed on the page for the former CEAlign Pluginhttp://www.pymolwiki.org/index.php/Cealign_plugin#References from before it was

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

Re: [PyMOL] ligand binding site visualisation

Hi James - You could put in a feature requesthttp://sourceforge.net/p/pymol/feature-requests/ to ask that non-canonical residues be included in the preset. In the meantime, the Property Selectorshttp://www.pymolwiki.org/index.php/Property_Selectors, Single-Word

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,

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

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

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.sourceforge.netmailto:pymol-users@lists.sourceforge.net Subject

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

the *distances* 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

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

:10 PM, Sampson, Jared jared.samp...@nyumc.orgmailto: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

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,

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

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 jared.samp...@nyumc.orgmailto:jared.samp...@nyumc.org: Hi James - I don’t have any experience with Profit. However, instead of using something like

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 modehttp://www.pymolwiki.org/index.php/Command_Line_Options. 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:

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,

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 alterhttp://pymolwiki.org/index.php/Alter and iteratehttp://pymolwiki.org/index.php/Iterate and a few

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

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

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

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

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] 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

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 - 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

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] 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

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

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,

Re: [PyMOL] using a pseudoatom for distance measurement

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 jared.samp...@nyumc.orgmailto:jared.samp

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

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

Re: [PyMOL] Pymol wrl output

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; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Pymol wrl output Hi, I tried it in white WRL as you suggested

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

. But the question is the same with above: how could I correctly label the bar according my data set? Best regards, Yeping -- 发件人：Sampson, Jared jared.samp...@nyumc.orgmailto: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 sunyep

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

Hi Yeping - I was about to suggest Sean Law’s new spectrumbarhttp://pymolwiki.org/index.php/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,

Re: [PyMOL] animation showing conformational change

Hi Yeping - With incentive PyMOL version 1.6 or later, you can use `morph`. From what I read at http://pymolwiki.org/index.php/Morph, you’ll need to put both conformations of the protein into one object, as different states. See http://pymolwiki.org/index.php/Load for more info on that.

Re: [PyMOL] boundaries/outlines of overlapping regions on surface

Hi Sid - I don’t think there is a way to accomplish this directly in PyMOL, but you can get partway there using the `ray_trace_mode` setting and named selections for the various regions you wish to depict. http://pymolwiki.org/index.php/Ray#Modes Ultimately, you’ll need to create a composite

Re: [PyMOL] Ligand surface: color issue after ray

Hi Tobias - It seems to me that you may not have hidden the lines/sticks from the object where you’ve shown the surface. For overlapping objects, the normal non-ray-traced view appears to give precedence to the object that was present in the viewer first. Try disabling and re-enabling your

Re: [PyMOL] Pymol insertion code

Hi Nick - This PDB employs non-standard usage of the PDB insertion code column. Typically, it is used to insert one or more residues between adjacent numbers in a canonically numbered structure, e.g. residue 42A (along with 42B, 42C, … , 42P, etc.) is between residues 42 and 43. As for

Re: [PyMOL] Pymol insertion code

Sorry - one quick correction to my previous email: On Mar 20, 2014, at 10:50 AM, Sampson, Jared jared.samp...@nyumc.org wrote: If you don’t need the cartoon representation to be continuous (e.g. if you’re zooming in on a different section of the protein you can replace the 3rd line

Re: [PyMOL] color each polymer chain differently

Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Mar 17, 2014, at 2:07 PM, Sampson, Jared jared.samp...@nyumc.orgmailto:jared.samp...@nyumc.org wrote: Hi Chandan - It seems like you're being limited by the 26 numbered colors in the util.cbc function

Re: [PyMOL] color each polymer chain differently

Hi Chandan - It seems like you're being limited by the 26 numbered colors in the util.cbc function. You could create your own randomized list of evenly-spaced colors, something like the following (untested, but should be approximately usable--sorry, I'm away from my computer today): from

Re: [PyMOL] Yaw, Pitch and Roll of CGO

Hi Pawel - If you can determine the primary axis of the cone from the tip and the center of the circle at the base, you can give `rotate` an arbitrary [x,y,z] float vector as its first argument instead of x, y or z. For example, if you generate your cone using something like the following

Re: [PyMOL] Yaw, Pitch and Roll of CGO

' option, what in did in 'rotate'. Moreover I should set 'origin=[X,Y,Z]' option as well as 'camera=0' in rotate option. Now it work smoothly and pretty nice ;) Thank you Paweł 2014-02-18 19:40 GMT+01:00 Sampson, Jared jared.samp...@nyumc.orgmailto:jared.samp...@nyumc.org: Hi Pawel - If you

Re: [PyMOL] selecting atoms ..

Hi Sampsa - The long list of ids crashes for me as well. Instead of listing each id separately, you can use ranges to define your selections. select paska, id 36-58 select isopaska, id 36-350 If you need to use non-continuous ids, you can use Boolean logic to join the ranges: select

Re: [PyMOL] generate solvent exclusive surface with scaled VDW radii

Hi Ye - The solvent excluded surface is the default surface representation in PyMOL. (Solvent accessible surface can also be generated using `set surface_solvent, on`.) View the surface with: show surface, myobj You can modify van der Waals radii like this: alter myobj, vdw=vdw*1.2 rebuild

Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

Hi Riccardo - Looking at the source (pymol/layer1/Ray.c, in RayRenderIDTF(), starting around line 2254) I can confirm that Sphere, Cone, Cylinder and Sausage representations are not implemented in the IDTF exporter. Currently only triangle mesh representations (cartoon, surface) are

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