Re: [PyMOL] Leap Motion

[Julian Heinrich]

Hi Tsjerk,

unfortunately I can't answer your question, but my former lab has done some
work with the leap motion to control molecular graphics that you might find
useful (not PyMOL though):
video: https://www.youtube.com/watch?v=XU_6TWM9ke8
paper: http://odonoghuelab.org/Publications/Sabir_2013.pdf

As you will see from the (non-representative) user study in the paper, it
can be tricky to get it to work more efficiently than keyboard + mouse for
many tasks. Let me know if you find it useful!

Cheers,
Julian

On Mon, Oct 3, 2016 at 2:40 PM Tsjerk Wassenaar  wrote:


Hey :)

We've been playing recently with a Leap Motion controller for PyMol and are
now wondering how we would emulate a mouse click event, based on the screen
coordinates. Does anyone know?

Thanks in advance,

Tsjerk

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Re: [PyMOL] Active site in Pymol

[Julian Heinrich]

Hi,

you can use the Measurement Wizard to get distances between atoms. PyMOL
will also print the residue type in the console if you click on any atom.

Best,
Julian


On Tue, Aug 23, 2016 at 8:45 AM Farzaneh Namazifar <
f.namazifar706...@gmail.com> wrote:

> Hi Dear all;
> I am a PyMol user.  I read the PyMOL tutorial
> 
>  about
> the hydrogen bond. I need some informations about hydrogen bond like:
> 1- length of hydrogen bond between two residue
> 2- which kind of residues are in the hydrogen bond
> 3- Number of hydrogen bond in active site
> As above, I need informations about  Hydrophobicity of residues in the
> active site. and else information about pi-pi interaction in DNA... I need
> your help ...
> Best Regards.
> Thank you in advance.
>
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Re: [PyMOL] error message for forster resonance calcualtor

[Julian Heinrich]

Hi Andina,

did you try to run 'import Forster_distance_calculator.py' from the Pymol
command line?
Have you tried to do 'run Forster_distance_calculator.py' instead, then
'forster ...' ?

Cheers,
Julian


On Mon, Sep 19, 2016 at 9:52 AM Andina Diana 
wrote:

> Hello everyone,
>
>
>
> I  have downloaded the newest version of pymol and wanted to run the
> script to calculate the Förster Resonance Energy distance R0 from the its
> wiki page (https://pymolwiki.org/index.php/Forster_distance_calculator) .
> When I import the file, it gives me following error message:
>
>
>
> Traceback (most recent call last):
>
>   File "C:\Program Files\PyMOL\\PyMOL/modules\pymol\parser.py", line 262,
> in parse
>
> exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>
>   File "", line 1, in 
>
>
>
> What should I do to not get this error message?
>
>
>
> Thank you for your help!
>
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Re: [PyMOL] Pymol Command window not displaying

[Julian Heinrich]

Hi,

are you trying to run PyMOL remotely, i.e. via ssh from your cluster?
This might work if you forward X11 to your local machine, though I'm not
sure if it supports OpenGL.

Looking at the error message, another possibility might be a missing tcl/tk
library?

Good luck,
Julian

On Tue, Sep 20, 2016 at 7:24 AM Srikanth Gumma 
wrote:

> Hi,
>
> Can anyone help me on this regard.
>
> Thanks
>
> -Srikanth.
>
> On Thu, Sep 1, 2016 at 10:19 PM, Thomas Holder <
> thomas.hol...@schrodinger.com> wrote:
>
>> Hi Srikanth,
>>
>> Is your custom Python installation properly set up with the custom Tcl/Tk
>> installation? Does the following work and open a Tk window?
>>
>> shell> /app/python/intel/2.7.12/bin/python # path guessed
>> python> import Tkinter
>> python> Tkinter.Tk()
>>
>> If not, then I think you need to set TCL_LIBRARY and/or TK_LIBRARY
>> environment variables first.
>>
>> Hope that helps.
>>
>> Cheers,
>>   Thomas
>>
>> On 31 Aug 2016, at 00:46, Srikanth Gumma  wrote:
>>
>> > Hi,
>> >
>> > I recently installed pymol from source using python-2.7.12 in my
>> cluster. I have to install python, tcl in a non standard location as this
>> is a cluster.
>> >
>> > After successful installation of pymol, I'm facing an issue while
>> opening pymol. I'm not able to see pymol command window, and receiving the
>> below error on the console.
>> >
>> > PyMOL(TM) Molecular Graphics System, Version 1.8.2.0.
>> >  Copyright (c) Schrodinger, LLC.
>> >  All Rights Reserved.
>> >
>> > Created by Warren L. DeLano, Ph.D.
>> >
>> > PyMOL is user-supported open-source software.  Although some
>> versions
>> > are freely available, PyMOL is not in the public domain.
>> >
>> > If PyMOL is helpful in your work or study, then please volunteer
>> > support for our ongoing efforts to create open and affordable
>> scientific
>> > software by purchasing a PyMOL Maintenance and/or Support
>> subscription.
>> >
>> > More information can be found at "http://www.pymol.org;.
>> >
>> > Enter "help" for a list of commands.
>> > Enter "help " for information on a specific command.
>> >
>> >  Hit ESC anytime to toggle between text and graphics.
>> >
>> >  Detected OpenGL version prior to 2.0. Shaders and volumes unavailable.
>> >  OpenGL graphics engine:
>> >   GL_VENDOR:   Intel
>> >   GL_RENDERER: Intel(R) HD Graphics 4600
>> >   GL_VERSION:  1.4 (4.0.0 - Build 9.18.10.3272)
>> > Traceback (most recent call last):
>> >   File "/app/python/intel/pymol/lib/python/pmg_tk/__init__.py", line
>> 35, in run
>> > PMGApp(pymol_instance,skin).run(poll)
>> >   File "/app/python/intel/pymol/lib/python/pmg_tk/PMGApp.py", line 323,
>> in __init__
>> > self.root = Tk() # creates the root window for the application
>> >   File "/app/python/intel/2.7.12/lib/python2.7/lib-tk/Tkinter.py", line
>> 1815, in __init__
>> > self.tk = _tkinter.create(screenName, baseName, className,
>> interactive, wantobjects, useTk, sync, use)
>> > TclError: invalid command name "tcl_findLibrary"
>> >  Detected 24 CPU cores.  Enabled multithreaded rendering.
>> >
>> >
>> > Appreciate any help to resolve the issue.
>> >
>> > -srikanth
>>
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>>
>>
>
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Re: [PyMOL] What's wrong with my pymol script?

[Julian Heinrich]

Hi,

adding a 'refresh' (http://www.pymolwiki.org/index.php/Refresh) seems to
work:

```
from pymol import cmd

cmd.fetch('1nmr', async=0)
for i in range(1, cmd.count_states()+1):
 cmd.set("state", i)
 cmd.png("%d.png" % (i), width=1000, height=1000, dpi=300)
 cmd.refresh()
```


On Sun, Aug 14, 2016 at 3:55 PM Dd H  wrote:

> Hi everyone,
> I want to render images of frames of my trajectory that loaded in pymol
> with the script below. After running this script, pymol outputs images
> and they are all the same. So what's wrong with my script?
>
> for i in range(1, cmd.count_states()+1):
>  cmd.set("state", i, "traj")
>  cmd.png("%d.png" % (i), width=10, height=10, dpi=300)
>
>
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Re: [PyMOL] difficulty using Python scripts in PyMOL

[Julian Heinrich]

Hi Mohsen,

I'm a Mac user and haven't installed PyMOL on Windows lately, but have you
tried following the installation instructions on the Wiki:
http://www.pymolwiki.org/index.php/Windows_Install ?

Cheers,
Julian

On Sun, Jul 31, 2016 at 5:28 PM Mohsen Chitsaz <
mohsen.chit...@flinders.edu.au> wrote:

> Hi all,
> I have difficulty using Python scripts in PyMOL. I cannot install PyMOL in
> a way that is compatible to Python. I initially installed Python 3.5.2, and
> then PyMOL 1.7.4. But PyMOL doesn't recognise a Python script file that I
> have created in NotePad++. I have put the file in PyMOL active directory,
> and run this command in PyMOL command line "run script.py".
> Can someone please help me with this?
>
> Cheers
> Mohsen
>
>
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Re: [PyMOL] Finding the surface residues using code

[Julian Heinrich]

Dear Leila,

you can download the respective script using the link shown on the top
right of the wiki page:
https://github.com/Pymol-Scripts/Pymol-script-repo/raw/master/findSurfaceResidues.py

Run this script in PyMOL by invoking 'run findSurfaceResidues.py' (using
the path you downloaded the script to).
Then you can run the functions explained on the wiki page.

Cheers,
Julian

On Mon, Jun 27, 2016 at 9:58 AM leila karami 
wrote:

> Dear Pymol users,
>
> I am using Pymol v 1.7.x. I want to obtain and show the surface residues
> in my protein.
>
> I found the following link:
>
> http://www.pymolwiki.org/index.php/FindSurfaceResidues#Usage
>
> How to run the code being in this link?
>
> Best,
>
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Re: [PyMOL] Help Download structural alignment

[Julian Heinrich]

Hi Clarisa,

you can save an alignment using the create and save commands, e.g.:

fetch 1oky 1t46, async=0
as ribbon
align 1oky, 1t46
create aligned, all
save aligned.pdb, aligned

You can also save the alignment in clustalw format, see
http://pymolwiki.org/index.php/Align.

I hope this is what you were looking for?

Cheers,
Julian


On Fri, Jun 24, 2016 at 3:10 PM Clarisa Alvarez 
wrote:

> Hi everyone:
> I am writing asking help to download the structural aligment performed in
> pymol.
> Thanks in advance.
> Regards,
> Clarisa.
>
> 2016-06-14 11:01 GMT-03:00 :
>
>> Send PyMOL-users mailing list submissions to
>> pymol-users@lists.sourceforge.net
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>> or, via email, send a message with subject or body 'help' to
>> pymol-users-requ...@lists.sourceforge.net
>>
>> You can reach the person managing the list at
>> pymol-users-ow...@lists.sourceforge.net
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of PyMOL-users digest..."
>>
>>
>> Today's Topics:
>>
>>1. Analysis of docking poses from 2 nmr-ensembles (James Starlight)
>>2. Re: Analysis of docking poses from 2 nmr-ensembles
>>   (Sampson, Jared M.)
>>3. Selective valency on bond (McIntyre, Patrick)
>>4. Re: Selective valency on bond (Andreas Warnecke)
>>
>>
>> --
>>
>> Message: 1
>> Date: Mon, 13 Jun 2016 15:41:58 +0200
>> From: James Starlight 
>> Subject: [PyMOL] Analysis of docking poses from 2 nmr-ensembles
>> To: pymol-users 
>> Message-ID:
>> <
>> caalqopzzjtykby+j_evphgvpp2_k_mhmv2holhjgf2d5pnr...@mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Dear Pymol users!
>>
>> I am studying protein-protein assosiation using 2 different proteins
>> as test case by means of variety of computational methods.
>> For my particular caseI need to compare binding poses emerged as the
>> result of protein-protein docking (ensemble 1: which  consists of 20
>> snapshots according to docking ranking) as well as MD simulation
>> (ensemble 2: which consists of 10 snapshots each of which represents
>> binding pose which has been established during long MD run).
>> Loading those two ensembles in pymol as 2 different models (in
>> NMR-like model format)  I need to performs some analysis  to find some
>> shared trends in each of them e.g RMSD of the distances between common
>> residues-pairs found in contact map analysis
>> or something else. What are most trivial suggestions might be in that
>> particular case?
>>
>>
>> Thanks for the suggestions!
>>
>>
>> James
>>
>>
>>
>> --
>>
>> Message: 2
>> Date: Mon, 13 Jun 2016 16:08:31 +
>> From: "Sampson, Jared M." 
>> Subject: Re: [PyMOL] Analysis of docking poses from 2 nmr-ensembles
>> To: James Starlight 
>> Cc: pymol-users 
>> Message-ID: 
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Hi James -
>>
>> First, it will be useful to split the states<
>> http://www.pymolwiki.org/index.php/Split_states>.
>>
>> split_states ensemble1
>> split_states ensemble2
>> delete ensemble1
>> delete ensemble2
>>
>> Then, superimpose all structures
>> onto a reference structure for easier visualization.  This won't affect
>> your distance measurements, but will make it easier to see the changes from
>> one object to the next.
>>
>> python
>> ref = 'ensemble1_0001'   # your reference object
>> for obj in cmd.get_names():
>> if obj != ref:
>> cmd.super(obj, ref)
>> python end
>>
>> For your residue pair analysis, you have to decide what kind of distance
>> you want to measure (e.g. CA-CA; average position of all atoms in the
>> residue; closest atoms, which would require looping through all atom pairs
>> in each residue pair and keeping only the shortest distance).  Then create
>> selection strings based on those criteria, use them in distance<
>> http://pymolwiki.org/index.php/Get_Distance> measurement, and print them
>> or add them to a variable to be output.  If you want to create and
>> visualize distance objects, use `distance` instead of `get_distance` and
>> pass a distance object name as the first parameter before the selections.
>>
>> python
>> sel1 = "resi 100 and name CA"
>> sel2 = "resi 200 and name CA"
>> sel3 = "resi 300 and name CA"
>> for obj in cmd.get_names():
>> d12 = cmd.get_distance("{} and {}".format(obj, sel1), "{} and
>> {}".format(obj, sel2))
>> d23 = cmd.get_distance("{} and {}".format(obj, sel2), "{} and
>> {}".format(obj, sel3))
>> print "{}: '{}' 

Re: [PyMOL] Getting Started

[Julian Heinrich]

Hi Melanie,

have you gone through the 'movie school' (
http://www.pymolwiki.org/index.php/MovieSchool) ?
I know that biomedical animators also like to work with the molecular
flipbook (https://www.molecularflipbook.org/) or bioblender (
http://www.bioblender.eu/).

Cheers,
Julian

On Wed, Jun 8, 2016 at 3:23 PM Melanie Prakash 
wrote:

> Hi!
>
> I was wondering what a good tutorial would be to start with learning
> PyMol. I understand basic movie making commands, but I want to move onto
> developing movies of more complex biological processes.
>
> Currently I'm in the process of understanding how to develop a movie of a
> phosphorylation, and I don't understand several of the commands and
> functions I'm supposed to use. At that level, does one mostly lean on their
> knowledge of PyMol (which is quite young) when designing a movie?
>
> Thanks!
>
> -Melanie
>
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Re: [PyMOL] Run pymol from source or compile?

[Julian Heinrich]

Hi Martin,

you need to compile PyMOL in order to see effects of code changes.
The installation instructions
 on the wiki
include some information on how to compile PyMOL from source.

Cheers,
Julian

On Tue, May 24, 2016 at 7:54 PM Martin Hediger  wrote:

> Can one run PyMOL from source (in order to see effects of changes to the
> source code whenever restarting) or can one only run a compiled version of
> PyMOL?
>
> Are there instructions for running from source?
>
> Best regards
> Martin
>
>
>
>
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>
>
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Re: [PyMOL] How to export secondary structure information from a PDB using PyMol?

[Julian Heinrich]

Hi,

in case you haven't solved this yet, the following command prints the
residue number and secondary structure:

iterate n. CA, print resi + ':' + ss

Cheers,
Julian

On Fri, May 13, 2016 at 10:40 PM ZHANG Cheng <272699...@qq.com> wrote:

> Dear PyMol friends,
> I would like to export the secondary structure of individual residues from
> a PDB. Can I ask if I can use PyMol to do that?
>
> I would like something like this:
>
> Residue 1: alpha-helix
> Residue 2: beta-sheet
> ..
>
>
>
> I think "http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py; can
> also do that. However, I found that one residue is loop in Pymol but is
> indicated as "strand" in the website. So I wonder if Pymol can output the 
> secondary
> structure of individual residues from a PDB?
>
> Thank you.
>
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Re: [PyMOL] Color coded script

[Julian Heinrich]

Hi,

are you referring to the code examples? I think the coloring scheme is just
a source code syntax highlighting, where all strings for example are in
red, comments are in green, and functions are blue.

Cheers,
Julian

On Tue, Nov 10, 2015 at 3:15 PM,  wrote:

> Hi,
>
> In the PyMolWiki under simple scripting parts of the command lines are
> color coded(red, blue and green). What does that mean?
>
> cmd.extend(“doSimpleThing”,doSimpleThing)
>
>
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Re: [PyMOL] Current and up to date manual

[Julian Heinrich]

Yes, the Wiki is the most current manual for non-subscribers, though it is
community driven and therefore not always up to date. If you point me to
outdated pages I'll try to fix them ASAP.

Cheers
Julian

On Sun, 8 May 2016, 00:09 Martin Hediger,  wrote:

> I found this manual page:
>
> http://pymol.sourceforge.net/newman/user/toc.html
>
> It says, its ancient and obsolete.
>
> Is the wiki the current and up to date manual?
>
> Is there a PDF manual anywhere?
>
> Many thanks
> Martin
>
> --
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>
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Re: [PyMOL] different distance calculated for same atoms

[Julian Heinrich]

Hi

You're passing more than one atom per selection to the cmd.distance()
function, in which case the function returns the average between the
measured distances (http://pymolwiki.org/index.php/Distance#PYMOL_API ).

On a side note, this could be done much simpler:
fetch 2nuz, async=0
h_add resn LEU and name CD1+CD2
set distance_exclusion, 4
distance , hydro, hydro, cutoff=5.0, mode=3
run
https://github.com/Pymol-Scripts/Pymol-script-repo/raw/master/get_raw_distances.py
get_raw_distances 

Cheers,
Julian

On Wed, May 4, 2016 at 11:48 PM, riddhiman sarkar <
riddhiman.sar...@gmail.com> wrote:

> Hello ,
> I am a new Pymol user. I am trying to calculate all the H-H distances
> between the methyl protons (CH3) in different Leucine residues in a
> protein, which are within 5A. For some reason, if I rerun the program with
> a distance threshold of 2A, I get different values for the same atoms. Here
> is the script that I am using. It would be great if someone can let me know
> what I am doing wrong.
> ***
>
> pymol.cmd.load('2nuz.pdb', '2nuz')
> pymol.cmd.disable("all")
> pymol.cmd.enable('2nuz')
>
>
> pymol.cmd.h_add("all")
> select1= '(neighbor 2nuz and resn LEU and (name CD1 or name CD2)) and (not
> elem c)'
> atoms = pymol.cmd.get_model(select1)
> select3= '(neighbor 2nuz and resn LEU'
> select4= ' and (name CD1 or name CD2)) and (not elem c) and name '
>
> for at in atoms.atom:
> x1=str(at.resi)
> v1= select3 + select4 + str(at.name)
> for at2 in atoms.atom:
> x2= str(at2.resi)
> v2= select3 + select4 + str(at2.name)
> if x1== x2:
> break
> elif x1 != x2:
> print
> str(at.resn)+str(at.resi)+'-'+str(at2.resn)+str(at2.resi),str(at.name
> )+'-'+str(at2.name), pymol.cmd.distance('',v1,v2,2.0)
> pymol.cmd.quit()
> **
>
> Here I get LEU10-LEU8 H01-H07 2.71310377121 if I use 5A in the distance
> command whereas I get LEU10-LEU8 H01-H07 1.78031635284 if I use 2A.
>
>
> Thanks a lot,
> Regards,
> Riddhiman Sarkar
>
>
>
>
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Re: [PyMOL] Appending a pdb file

[Julian Heinrich]

Hi Mohsen,

if you want to superimpose structures, have a look at the align command:
http://pymolwiki.org/index.php/Align

Cheers,
Julian

On Thu, Feb 18, 2016 at 10:47 PM, Mohsen Chitsaz <
mohsen.chit...@flinders.edu.au> wrote:

> Hi
>
>
>
> In order to superimpose two protein sequences, I am trying to append a pdb
> file to an existing protein sequence, which I have already opened in PyMol.
> The append function is not working in my PyMol. Could someone help me with
> this please.
>
>
>
> Cheers
>
> Mohsen
>
>
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Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

[Julian Heinrich]

Hi all,

translate does seem to work with CGOs if you use named arguments (note the
'object=' in the argument list):

cmd.translate([x,y,z], object='membrane')

Here's an example that you can copy and paste into pymol:

---
python

from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
   CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
   CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
   CYLINDER, 0., 0., 0., 0., 0., 10., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
   ]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[10.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,10.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,10.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')

# here we translate it
cmd.translate([1,0,0], object='axes')

-

the axes should then be translated by 1 unit to the right.

Cheers,
Julian

On Wed, Feb 3, 2016 at 6:55 AM, Sampson, Jared M.  wrote:

> 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 current one,
> then applying it to the object using cmd.set_object_ttt().
>
> Alternatively, if you can reproducibly identify any vector that should be
> perpendicular to the membrane, you could use those points as the start and
> end points for your initial load_cgo command.  For example, if your
> receptor happens to have a symmetric channel, something like this might
> work.
>
> ```
> # create pseudoatoms at the average positions of residues at the top and
> bottom of the chain
> pseudoatom top,  and n. CA and chain
> A+B+C+D
> pseudoatom bot,  and n. CA and chain
> A+B+C+D
>
> # Orient to the pseudoatoms and fine tune the positions along the viewport
> Y axis.
> # (Make sure you don't move the view until you're done positioning the
> pseudoatoms.)
> orient (top or bot)
> turn z, 90  # assuming `orient` put them along X and you want them along Y
> translate [0, 2, 0], top
> translate [0, -1.5, 0], bot
>
> # Get the coordinates of the two end points
> from pymol import stored
> stored.start = []
> stored.end = []
> iterate_state 1, top, stored.start = (x,y,z)
> iterate_state 1, bot, stored.end = (x,y,z)
>
> # Create the CGO cylinder (I made it semitransparent)
> from pymol.cgo import ALPHA, CYLINDER
> x1,y1,z1 = stored.start
> x2,y2,z2 = stored.end
> r1,g1,b1 = 1, 1, 0
> r2,g2,b2 = 1, 1, 0
> radius = 100
> cmd.load_cgo([ ALPHA, 0.5, CYLINDER, x1, y1, z1, x2, y2, z2, radius, r1,
> g1, b1, r2, g2, b2 ], "membrane")
>
> ```
>
> Not sure if that will be applicable to your use case, but hopefully it
> will at least give you an idea of one approach that could work.
>
> Hope that helps.
>
> Cheers,
> Jared
>
> --
> Jared Sampson
> Columbia University
>
>
> On Jan 29, 2016, at 4:33 PM, Honegger Annemarie 
> wrote:
>
> I am trying to show some cell surface receptors and to indicate their
> position relative to the membrane.
>
> I thought to indicate the plane of the membrane by a flat disk, a ago
> cylinder.
>
> x1,y1,z1 = 0, -1, 0 # start point
> r1,g1,b1 = 1, 1, 0 # color (yellow)
> x2,y2,z2 = 0, -2, 0 # end point
> r2,g2,b2 = 1, 1, 0 # color (yellow)
> radius = 100
> cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2,
> b2 ], "membrane" )
>
> When I try to move this cylinder into the correct position
> with cmd.transform_selection,
> using the transformation parameters extracted from get_view (reordering
> them as needed)
> I get the error message "Selector-Error: Invalid selection name “membrane”
> “
>
> The same transform command works fine if I apply it to a pseudo atom
> originally generated with coordinates 0,0,0.
>
> Any suggestion how else I could indicate the membrane, or how I could
> place my ego object parallel
> to the screen yz plane? I have to be able to do this in a reproducible
> fashion, as I have to  do this
> for a large number of constructs that bend my receptors relative to the
> membrane in various ways.
>
> Thanks for your help
> Annemarie
> ___
>
> Dr. Annemarie Honegger PhD
> Department
> of Biochemistry
> Zürich University
> Winterthurerstrasse 190
> CH-8057 Zürich
> Switzerland
>
>
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Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

[Julian Heinrich]

Hi Annemarie,

Have you tried the following?
cmd.translate([x,y,z], object='membrane')

replace x,y,z with your translation vector.

Cheers,
Julian

On Sat, Jan 30, 2016 at 8:33 AM, Honegger Annemarie 
wrote:

> I am trying to show some cell surface receptors and to indicate their
> position relative to the membrane.
>
> I thought to indicate the plane of the membrane by a flat disk, a ago
> cylinder.
>
> x1,y1,z1 = 0, -1, 0 # start point
> r1,g1,b1 = 1, 1, 0 # color (yellow)
> x2,y2,z2 = 0, -2, 0 # end point
> r2,g2,b2 = 1, 1, 0 # color (yellow)
> radius = 100
> cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2,
> b2 ], "membrane" )
>
> When I try to move this cylinder into the correct position
> with cmd.transform_selection,
> using the transformation parameters extracted from get_view (reordering
> them as needed)
> I get the error message "Selector-Error: Invalid selection name “membrane”
> “
>
> The same transform command works fine if I apply it to a pseudo atom
> originally generated with coordinates 0,0,0.
>
> Any suggestion how else I could indicate the membrane, or how I could
> place my ego object parallel
> to the screen yz plane? I have to be able to do this in a reproducible
> fashion, as I have to  do this
> for a large number of constructs that bend my receptors relative to the
> membrane in various ways.
>
> Thanks for your help
> Annemarie
> ___
>
> Dr. Annemarie Honegger PhD
> Department
> of Biochemistry
> Zürich University
> Winterthurerstrasse 190
> CH-8057 Zürich
> Switzerland
>
>
>
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Re: [PyMOL] superimposition of 2 ligand molecules

[Julian Heinrich]

Hi,

have a look at the 'align' command:
http://pymolwiki.org/index.php/Align

Best,
Julian

On Thu, Jan 28, 2016 at 7:13 AM, leila karami 
wrote:

> Dear pymol users,
>
> I have 2 ligand molecules having similar backbone. There is little
> difference between them. When I load them in pymol, I have following figure:
> https://www.dropbox.com/s/k4g53p0qoxp58zs/pymol.png?dl=0
>
> I want to have these 2 ligands in superimposed form such as following:
> https://www.dropbox.com/s/v75uhrghy4johjy/pymol_2.png?dl=0
>
> Please guide me to do that.
>
> Best,
>
>
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Re: [PyMOL] on PDB display and calculation

[Julian Heinrich]

Hi Smith,

are you looking to visualize symmetrie axes? Then this might be a starting
point:
http://www.pymolwiki.org/index.php/SuperSym

Cheers,
Julian

On Mon, Nov 23, 2015 at 4:15 PM, Smith Liu  wrote:

> Dear All,
>
> Once I have displayed a tetramer PDB by pymol, is any way I can get the
> central axis of the tetramer and display it? Is any way I can get the
> cross-section of the tetramer (perpendicular to the central axis) and
> display it? If the tetramer is asymmetric, then how to get the central axis
> and cross-section？
>
> Smith
>
>
>
>
>
>
>
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Re: [PyMOL] on coloring residues based on residue conservation

[Julian Heinrich]

Hi Smith,

if you have a value for the conservation for each residue, you can use the
spectrum command as described here:
http://www.pymolwiki.org/index.php/Spectrum
to color residues by that value. In the 'intermediate' example, replace
newB with your value for conservation.

Hope this helps.

Cheers,
Julian

On Mon, Nov 16, 2015 at 4:55 PM, Smith Liu  wrote:

> Dear All，
>
> Is any simple method by pymol we can color residues based on the residue
> conservation?
>
> Best regards.
>
> Smith
>
>
>
>
>
> --
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