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

es. National Institute of Allergy and Infectious > Diseases shall not accept liability for any statements made that are sender's > own and not expressly made on behalf of the NIAID by one of its > representatives. > > From: Sean Law mailto:magic...@hotmail.com>> > Date:

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

different colors to indicate your SS assignments in another cartoon mode? Cheers, Jared Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jun 4, 2014, at 1:50 PM, Sean Law wrote: Hi PyMOLers, I have a c-alpha only model and I wou

[PyMOL] Visualize Sheets from C-alpha Only Structure

Hi PyMOLers, I have a c-alpha only model and I would like to visualize both helices and sheets based on my own custom SS assignments (via "alter"). Altering a residue's SS assignment to helix or loop (ss="H" or ss="L") is fine and can be visualized. However, altering a residue's SS assignment to

Re: [PyMOL] show color bar with b-factor

You can try the spectrumbar script: http://www.pymolwiki.org/index.php/Spectrumbar Best, Sean -- "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your

[PyMOL] Draw Ellipsoid

Hi PyMOLers, I am trying to use the built-in functionality to draw a user-defined ellipsoid and I am doing this by adding an extra ANISOU line in my PDB. Here is a test case: ATOM 2 CA ALA D 500 -1.217 1.844 -2.065 1.00 1.00 CAANISOU2 CA ALA D 50026170 51470

[PyMOL] mapping atom names between molecules

I too have encountered a similar problem and was hoping that somebody had a suggestion for this. I've tried using CEALIGN to attempt to align the molecules and then hoped that I could simply use some atom-atom pairwise distances to map one set of atoms onto another but CEALIGN doesn't seem to

[PyMOL] Usage Specification

Hi PyMOL Community, I have a PyMOL script that I have written that starts with the following kind of format: -from pymol import cmdfrom re import * def test (*args, **kwargs): var1=0 sel="" for key in kwargs:if (key == "var1"): var1=int(kwargs["var1"]) elif (key

Re: [PyMOL] Update Selection From Frames

Takanori, I've tried the following: for a in range(1,8): cmd.mdo(a,"hide sphere; select test, input_object_name & c. b & i. 19 around 4 & resn HOH; show sphere, test") where "HOH" is the residue name for water (so I want to know only the waters within a 4 Angstrom radius of residue number 19). H

Re: [PyMOL] Update Selection From Frames

Takanori, Thanks for pointing that out! I might be misunderstanding the usage but it does seem a bit tedious to have to go through each frame (if I had 1000+ frames) and then make a selection. I'm hoping that this isn't the only solution and that there's some other setting/command that I can use

[PyMOL] Update Selection From Frames

Hi PyMOLers, I was wondering if it were possible to have a selection update itself for every frame. Specifically, I have a simulation trajectory of a protein in a water box and I want to show only the waters that are within 5 Angstroms of the protein binding site. Obviously, as the trajectory

Re: [PyMOL] MacPyMOL Knowledge of Opened Structures

Jason (and PyMOLers), To clarify, B.dcd matches the number of atoms in B.pdb and A.dcd also matches the number of atoms in A.pdb. In the previous example, if I perform steps 3 and 4 first then it works in loading B.dcd into object "B". Then, if I try to open up A.pdb into a separate PyMOL win

[PyMOL] MacPyMOL Knowledge of Opened Structures

Hi PyMOLers, I noticed some strange behaviour when I do the following: 1) Load A.pdb into MacPyMOL via "pymol A.pdb"2) Load a CHARMM simulation trajectory into object "A" via "load A.dcd, A" 3) Load a completely different structure (must have different number of atoms than A.pdb), B.pdb, into a

[PyMOL] movie_panel on OSX

Hi PyMOLers, I have set "movie_panel=1" in MacPyMOL but I don't see the normal movie controls as in the Windows version of PyMOL which is typically situated below the viewing area. Can somebody tell me where it went? Thanks Sean -

[PyMOL] jump.py - fails to set key on Mac

Hi PyMOLers, I had written a script called jump.py which is used to jump between frames after loading in a trajectory: http://www.pymolwiki.org/index.php/Jump Originally, I was using this on a PC and am now on a MAC (at work). For some unknown reason, the default key "PgDn" doesn't seem to resp

Re: [PyMOL] Reading Protein Structure File (PSF)

...@gmail.com To: magic...@hotmail.com CC: pymol-users@lists.sourceforge.net Hi Sean, The .psf file format is for a topological desription (bonds, angles, etc), not for coordinates afaik. Cheers, Tsjerk On Dec 7, 2011 6:25 PM, "Sean Law" wrote: Hi PyMOLers, Can anybody tell me if

[PyMOL] Reading Protein Structure File (PSF)

Hi PyMOLers, Can anybody tell me if there's a way to read in a protein structure file (PSF). This is a common file format in simulation programs such as CHARMM and NAMD and basically gives similar information to the PDB file. Any suggestions would be greatly appreciated. Thank you for your time

[PyMOL] Show Sticks - Turns Molecule Blue

Hi PyMOLers, I have tried installing both PyMOL 1.3 and PyMOL 1.4.1 on OpenSuse (old Pentium 4) and am finding that when I load a molecule and click "Show --> Sticks" that the entire molecular gets colored blue (originally the green default lines color). After trying to change the color (Colo

Re: [PyMOL] Script for Torsion angles

If you find that get_dihedral is slow then you can try using the code from pucker.py which contains a section on calculating dihedrals for the nucleotide sugar pucker: http://pymolwiki.org/index.php/Pucker Sean

[PyMOL] movie.produce

Hi PyMOLers,Can somebody offer an explanation for the possible values that can be used with the "movie.produce" command?produce filename [, mode [, first [, last [, preserve [, encoder [, quality [, quiet ]]]Any clarification of the scope of each option would be appreciated.ThanksSean

Re: [PyMOL] PyMOL-users Digest, Vol 60, Issue 7

Hi PyMOL Community, I have a trajectory file loaded into PyMOL but I would like to play the movie in reverse order. Is there a way to achieve this within PyMOL? I know that I could do this by outputting the states as PNG files and then reversing them in an external program but I would like to

Re: [PyMOL] Center of Mass

Cunliang, There is a script available on the PyMOL-Wiki that calculates either the center-of-mass OR the center-of-geometry. Please see http://www.pymolwiki.org/index.php/Center_Of_Mass It uses the "pseudoatom" function to generate a sphere at the desired center of mass. Hope this answers yo

Re: [PyMOL] Independent Zooming in Grid Mode

Hi, That was my first instinct as well and I tried that. However, the problem is that rotating the molecules gets very tricky since the molecules are now no longer in the same plane. So, if I translate one of them either towards or away from me and then rotate, that molecule will rotate away

[PyMOL] Independent Zooming in Grid Mode

Hi PyMOLers, I was wondering if anybody had a solution for independent when using grid_mode=on. I want to be able to show, side-by-side, the same structure where one structure is "zoomed in" on a specific part on the biomolecule and the other object is "zoomed out" (viewing the entire molecule

[PyMOL] Atom Numbering

Hi PyMOLers, Is there a way to display PDB atom numbers when you right click on an atom? It normally gives information like object/segment/chain/resn/resid/name but I want a quick way of comparing the atom number with the PDB atom numbering. Thanks! Sean

Re: [PyMOL] Builder Bug

Hi PyMOLers, I managed to figure out what the problem was. Although I was generating the short peptide without any problems using PyMOL, the name that was I saving the PDB file to was called "ala2.pymol.pdb" and I guess PyMOL didn't like this name (omitting the ".pymol" part fixed the problem

[PyMOL] Builder Bug

Hi PyMOLers, Can anybody confirm the following bug in PyMOL's builder? 1) Open PyMOL 2) Issue "Alt-A" twice to generate a two residue peptide of alanine-alanine 3) Save the molecule 4) Close PyMOL 5) Use PyMOL to view saved molecule For some reason, I can't view the molecule and is giving me an

[PyMOL] object matrix not updated with pair_fit

Hi PyMOLers, I was wondering if this problem was exclusive for my case. I was using "pair_fit" (rather than super/align) to superimpose two conformations of the same structure and noticed two things: 1) After being superimposed, BOTH structures (source and target) end up moving rather than j

Re: [PyMOL] Delete states function?

Jason, Being a complete novice when it comes to movie making, I decided to finally take the plunge. First, I tested your commands on the prototypical 1nmr file which worked great with the commands that you had described. However, when I tested the same commands on a 212 state DCD file the re

[PyMOL] Set cartoon_transparency bug?

Hi PyMOLers, I think there is a bug in PyMOL regarding the "set cartoon_transparency" setting. According to the PyMOL-Wiki, the arguments are: set cartoon_transparency, value, selection where the "value" ranges from 0.0-1.0 and the selection is optional. However, selections that are not ent

[PyMOL] CGO Color

Hi PyMOLers, I'm not sure if this is a bug or not but when I draw CGO shapes in PyMOL and then later decide to give the shape a different color, I can't seem to change the color of the CGO object by simply clicking on "C" from the internal GUI and selecting the desired color. Instead, I need

[PyMOL] Citing PyMOL

Hi All, According to the newly upgraded PyMOL website, the correct method for citing PyMOL is: The PyMOL Molecular Graphics System, Version 1.3, Schrödinger, LLC. However, I'm finding it difficult to choose a category in Endnote so that the format comes out as shown above. I know that this

[PyMOL] Modevectors.py Bugs Fixed

Hi All, I just wanted to let everyone know that there were some minor bugs in the modevectors.py script (originally written by me) that were discovered (and debugged) by a fellow PyMOLer (Raul Mendez). These bugs only affected the usability of the script and should not affect the output. I h

[PyMOL] Ray Trace Triangles

Hi PyMOLers, I have been tackling this problem (on and off) for quite some time now but without any luck. I have been trying to create CGO triangles using the following simple sample script: ### from pymol.cgo import * from math import * from pymol import cmd

[PyMOL] MPEG Movies in PyMOL

Hi All, I was wondering if anybody knew how to save MPEG movies in PyMOL via command line (I am using v1.3). I understand that movies can be saved via File->Save Movie As->MPEG but I want a full screen sized movie (full screen mode) where only commands issued via command line can be accessed

[PyMOL] Center-of-Mass

Hi All, I have re-written the center-of-mass script found on the Wiki (which was actually only calculating center-of-geometry). This script provides three improvements to the previous script: 1) The real center-of-mass can be calculated based on a table of atomic masses, 2) pseudoatoms are us

[PyMOL] PyMOL Print Limitation

Hi All, I noticed that when I write a script that prints something in PyMOL that there appears to be a limitation to the continuous length that can be printed to the external GUI. Here is an example script: # from pymol import cmd def testing (): out=

[PyMOL] Jumping Frames

Hi All, I have written a quick little script to jump through various frames from an MD simulation loaded into PyMOL: ### from pymol import cmd import time def jump (*args, **kwargs): #Example: jump 1, 10, 20 #This will jump from frame 1

[PyMOL] Transparency vs. Selection

Hi All, I'm not sure if this is a bug in PyMOL but I found that when you make a selection, show it as spheres representation, and then turn on the transparency (to anything but "off"), none of the now transparent spheres be selected via a mouse-click in the viewing area. Thus, if I selected

Re: [PyMOL] New Feature Ideas

Hi all, Being a user of Adobe products, I am use to having a very customizable working environment so that you could easily improve overall workflow and decrease fumbling time. I find myself wanting my productivity to increase when using PyMOL. While I do input a lot of my commands by hand,

Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 5

Hi, Another idea that came to mind while staring at MD trajectories all day is the ability to display measured values (distance, angle, dihedral, etc) in a localized or boxed in area (maybe even under the list of objects). The main use for a measurement area would be to make it easier to moni

Re: [PyMOL] New Feature Ideas

Hi all, Another feature that I find myself always wanting is a "kill script" button and/or command. This comes in handy when I am testing a new python script and, accidentally, throw in an infinite loop. It would be nice to have some sort of kill switch not only for python scripts but even f

Re: [PyMOL] New Ideas

Is it possible to include a function that could easily add or delete states (from the beginning, middle, or end of a set of states)? Something with the following syntax: delete_states 14 #Deletes state 14 delete_states 10-20 #Delete states 10-20 d

[PyMOL] CEalign - PyMOL Build

Jason, I would LOVE to see CEalign built along with PyMOL. +1 Sean _ Say Happy New Year with Messenger for Mobile. http://go.microsoft.com/?linkid=9706117-

[PyMOL] Feature Requests/Ideas

Jason, Here are some features that I have discussed with Warren in the in the past: 1) Vector graphics output (preferably in Adobe Illustrator format, SVG, postscript, or PDF format). I tend to make all of my posters and publication figures in Adobe illustrator (due to its scalability) and im

[PyMOL] Align each state to another reference structure

Hi All, I have two structures that are homologous. One structure #1 contains 100 states and structure #2 contains only one state. I would like to align each state of structure #1 to structure #2 based upon some selection. From what I can understand, if I say: align struct1, struct2 This w

[PyMOL] Spectrum

Robert, I would have to agree with you. I've used many of your scripts and have also learned a lot from them and think that the color B script is pretty robust and helpful. I could be wrong but I remember the original poster commenting about using the "min & max" settings from the spectrum c

[PyMOL] spectrum

Mark, Sorry for the earlier confusion. I think I found a hackish way of getting a gray spectrum: To specify a particular color spectrum you need to know the language of the spectral ranges. These ranges are discussed briefly in the PyMOL-Wiki (spectral range colors): http://www.pymolwiki.o

Re: [PyMOL] Replace Coordinates in State

rate_state and alter_state are highly inefficient – it would make more sense to provide a means of exporting and re-importing coordinate sets via either native Python lists or, even better, NumPy arrays. In what form do you have the current coordinate data? Cheers, Warren From

[PyMOL] Replace Coordinates in State

Hi All, I was wondering if there was a faster way to replace all coordinates. I've used commands such as iterate_state and alter_state before but they are far too slow since they have to iterate over each atom. Instead, I want to replace one set of coordinates that correspond to a specific s

Re: [PyMOL] Export trajectory

rently than your original PDB. There are two ways around this, 1) Save a corresponding PDB file for that trajectory that is renumbered by PyMOL or 2) Retain the RESID (see PyMOL-Wiki) Since this was done on a whim, please use at your own risk until it i

Re: [PyMOL] Iterate Script Over States

I think I figured it out (though, it wasn't documented). What I needed was to use: cmd.get_model(selection, STATE) I think that's the correct usage? What I needed was to loop through a selection and then to calculate the sugar pucker information. However, not all atoms from the selection a

[PyMOL] Iterate Script Over States

Hi PyMOL Users, I was wondering if there was a smart way of having a script iterate over all (or some) of the states. I know that there are the usual iterate and iterate_state commands available but it appears that it makes for clumsier code. More specifically, I'm looking to use the pucker.

Re: [PyMOL] Display vectors of some atoms by arrow? (S4C6Ar Chung)

Oscar, If you visit the PyMOL-Wiki, you will find a script called "modevectors.py": http://www.pymolwiki.org/index.php/Modevectors There are several examples there that will allow you to customize the arrows. Sean > Dear all, > > Is it possible to show normal model/vectors of the "selected

Re: [PyMOL] PyMOL-users Digest, Vol 39, Issue 4

I was wondering if AxPyMOL could handle a .pse file that loaded two pdb structures in powerpoint. I've simply created a .pse file by fetching 2bmv and 2hhb. Then I loaded this onto my PC laptop while in powerpoint. Other slides in the same presentation with a single pdb file works fine. How

[PyMOL] Python Function with Unlimited Positional Arguments

Hi PyMOLers, I am trying to write a python script that will allow a user to provide an unlimited number of positional arguments for a function. I am use to the following scheme for defining a function and its arguments: def some_function ( x, y, z, file="false"): #DO SOMETHING return Where

[PyMOL] DCD Trajectories and Movie Panel

Hi all, I am playing around with the new PyMOL 1.2 release and was hoping to use the Movie Panel in conjunction with a loaded DCD trajectory file. However, after loading the MD trajectory and setting "movie_panel" to 1 I don't see the prescribed time line below the viewing area. Of course, i

Re: [PyMOL] Principal Axes of Rotation

nt in the X Y planes should be invariant to 180 degree rotations about the Y or X axes respectively. Cheers, Warren From: Sean Law [mailto:magic...@hotmail.com] Sent: Wed 6/3/2009 12:28 PM To: matthew.frank...@imclone.com Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Princip

Re: [PyMOL] Principal Axes of Rotation

gt; CC: pymol-users@lists.sourceforge.net > From: matthew.frank...@imclone.com > Date: Wed, 3 Jun 2009 15:13:25 -0400 > > > > Sean Law wrote on 06/03/2009 12:52:45 PM: > > > Warren, > > > > After a deja vu moment, I realized that I had posed a similar > > ques

Re: [PyMOL] Principal Axes of Rotation

; structure that minimises the distance of all the points to it. Or, to > put it another way, the least-square-plane through the structure, the > normal to that plane, and a thir axis perpendicular to both. > > If this is the case, you are in luck, as I already made such a thing: > &g

[PyMOL] Principal Axes of Rotation

Hi, For the past couple of days I've been trying to find a way to rotate an object in order to show a front and side profile for publication. However, rotating with respect to the x, y, or z axes does not produce the correct result (even after moving the center-of-mass of the structure to the

[PyMOL] Load Selection

Hi PyMOLers, I was wondering if there is a way to load part of a PDB file if you know a priori what you want thereby saving time/memory? Currently, I have a system that is ~160,000 atoms (protein-DNA complex with explicit water molecules taken from an MD simulation). When I load more than 10

[PyMOL] POVRAY Usage

Hi All, While ray tracing a scene with 10 x-large proteins in grid mode at 3600, 3600 (width, height) I ran out of RAM (2 GB). I tried it again by writing everything into a script and using pymol -qc which still ran out of memory. I read somewhere that POVRAY is less of a memory hog so I ins

[PyMOL] Vector-Based Figure Export

Hi Warren, I know that there has been some discussion on implementing a vector-based figure export. I was wondering if there were any updates on this? I think that this would be an amazing feature to have. Thanks! Sean _ Inter

Re: [PyMOL] creating arrows

Hi Bala, Recently, I added a new python script to the PyMOLWiki. Search for "modevectors" or "arrows" and you should find the method for drawing arrows with TONS of examples. I'm not sure if that's what you are looking for but you should be able to find your answer amidst the script. Sean

[PyMOL] CGO Cones

Hi, I noticed that version 1.1 is said to have "Cone representation available as cgo" so I downloaded the windows binary and tested it out but I haven't been able to get it to work. Any clarification on how to get this to work would be greatly appreciated. A sample code is written below. Se

Re: [PyMOL] get_dihedral bottleneck

thier) is below. Sean from pymol.cgo import *# get constants from math import * from pymol import cmd def pucker(selection): # Author: Sean Law # Institute: Michigan State University # E-mail: s...@msu.edu obj_name = selection objects = cmd.get_names(selection) fo

[PyMOL] get_dihedral bottleneck

? Thanks in advance! Sean = from pymol.cgo import *# get constants from math import * from pymol import cmd def pucker(selection): # Author: Sean Law # Institute: Michigan State University # E-mail: s...@msu.edu