pymol-users Mailing List for PyMOL Molecular Graphics System

Hi everyone!

I am new to this list. I am trying to download pymol on ubuntu 14.04. I
installed the required dependencies but when i run python.py setup build, I
get an error that C++ failed with the exit. installation terminated. please
help me out of this problem. The screen shot of the error is attached.
Thanks in advance.

Regards
Neelam

Hi there people

When I download some structures (e.g. like insulin, PDB 1trz) I get what it
seems a duplicated rendering, is that right?

I've got this kind of issue (??) a while...

Please let me know.

Hi Jenny,

Try this fixed version of the plugin:

http://pymol.org/tmp/kvfinder_pymolplugin_linux.py

Cheers,
  Thomas

> On Feb 8, 2018, at 11:27 AM, Jennifer Miles <J....@le...> wrote:
> 
> Hi all,
> 
> I'm Jenny and I am new to this list. If anyone can help I would be very thankful. 
> 
> I am trying to install the plugin KVFinder on the newest version of PyMOL with a Microsoft Surface running Windows 10. I have set up the environment  variable is detailed in the installation guide 
> shaker.umh.es/computing/24938294-IG.pdf and set up in the plugin using the plugin manager but every time I try to open it I get the error below. 
> 
> Unable to initialize plugin 'kvfinder_pymolplugin_windows' (pmg_tk.startup.kvfinder_pymolplugin_windows).
> Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x0000000005235588>> ignored
> 
> Any help would be much appreciated :)
> 
> Jenny
> 
> Dr Jennifer Miles
> Postdoctoral Research Fellow
> School of Chemistry
> University of Leeds
> 
> LS2 9JT Leeds, UK
> phone: +44 (0) 11334 36578
> email: j....@le...

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi all,


I'm Jenny and I am new to this list. If anyone can help I would be very thankful.


I am trying to install the plugin KVFinder on the newest version of PyMOL with a Microsoft Surface running Windows 10. I have set up the environment  variable is detailed in the installation guide

shaker.umh.es/computing/24938294-IG.pdf and set up in the plugin using the plugin manager but every time I try to open it I get the error below.


Unable to initialize plugin 'kvfinder_pymolplugin_windows' (pmg_tk.startup.kvfinder_pymolplugin_windows).

Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x0000000005235588>> ignored


Any help would be much appreciated 😊


Jenny


Dr Jennifer Miles
Postdoctoral Research Fellow
School of Chemistry
University of Leeds

LS2 9JT Leeds, UK
phone: +44 (0) 11334 36578
email: j....@le...

Hi Fernando,

Can't find any bad english in your email :-)

1: https://en.wikipedia.org/wiki/Marching_cubes

2: To open the isomesh again in PyMOL, I suggest to save a PyMOL session file (.pse). Getting access to the actual geometry is more tricky. There is a script on the PyMOLWiki which can convert isomesh and isosurface objects to CGOs. The script could be a starting point for you to export a custom file. The data is rather simple, just a sequence of vertices and normals.
https://pymolwiki.org/index.php/Dump2CGO

3: VTK? scikit-image?

Cheers,
  Thomas

> On Feb 5, 2018, at 4:24 AM, Fernando Oliveira <fll...@gm...> wrote:
> 
> Hi!
> 
> This is my first e-mail to this list. Sorry in advance for my bad english.
> 
> I've been using APBS for the past month in order to build protein binding sites representations for a artificial neural network I've been working on. 
> At first I used the OpenDX output file from APBS stand-alone but I wanted to generate Isomesh files aswell, in order to store the files conveniently for future analysis or even to use as data input at some order work.
> 
> 1- When APBS finished calculation, it creates a map object. But how does PyMol translate the .dx map into that beautiful Isomesh? (achievable using the Isomesh command aswell)
> 
> 2- How to save that isomesh in a way I could open it again with Pymol or another Visualization tool? (I already tried saving as .wrl. but I cannot open it on Pymol and the file syntax is confusing)
> 
> 3- Are there any other softwares or libraries to do such things? (output isomesh at one specific level (5), store it in a convenient way, etc)
> 
> Thanks for the attention.

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Maria,

If the load command fails, then you don't have the correct "working directory". You can query PyMOL's working directory with the "pwd" command and change it with "cd". See:

https://pymolwiki.org/index.php/Pwd
https://pymolwiki.org/index.php/Cd

Or more easily from the PyMOL 2.0 menu: "File > Working Directory > Change..."

Loading session files "partially" has also become even easier in PyMOL 2.0. Just use "File > Open...", after browsing for your .pse file PyMOL will show a dialog where you can choose to load partial or not.

Cheers,
  Thomas

> On Feb 6, 2018, at 12:46 PM, COSTA Maria <mar...@i2...> wrote:
> 
> Dear PyMOL users,
>  
> I would like to combine two pymol sessions together to compare to different conformations of a molecule that I have in two different pse files.
>  
> One of you suggested me the following (and this works with others)
>  
> load session1.pse
> load session2.pse, partial=1
>  
> but in my case, when I open a new pymol session and type : load nameofmysession.pse I get an error saying ‘can’t open  nameofmysession.pse’ ? Is this because pymol doesn’t find my pse  file in my computer ? If yes, where should I store my pse session files ?
>  
> Also, regarding how to proceed: Should I open a new pymol session and type the two command lines above successively ? For example, should I type “load session1.pse” first, hit enter and then type ‘load session2.pse, partial=1’ ??
>  
> Many thanks for your help,
>  
> Maria

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

We've closed the poll. Thanks to everyone who participated!

The result wasn't quite what I was hoping for ;-) The clear winners are "protein" and "nucleic". But I also got direct feedback that adding "protein" as a keyword would introduce backwards incompatibility with exiting workflows, where "protein" is used as an object or selection name.

So this is what's we'll do:
1) add "polymer.protein" and "polymer.nucleic" as the new keywords (place #2 in the poll)
2) let PyMOL print a deprecation warning if "protein" or "nucleic" are used as names, we may want to add them as keywords in the future

The new keywords are available in SVN rev 4185 and in the latest alpha build (https://pymol.org/alpha ). The PyMOLWiki selection algebra page has been updated.

Cheers,
  Thomas

> On Dec 18, 2017, at 7:41 PM, Thomas Holder <tho...@sc...> wrote:
> 
> We'd like to know your thoughts!
> 
> How should we name the new selectors for protein and nucleic acid?
> 
> Link to poll:
> https://goo.gl/forms/r0Ck03VTytZQxN4A2
> 
> We will enhance the PyMOL selection language by adding a new selector for protein, and a new one for nucleic acid. They will be subsets of the already existing "polymer" selector.
> 
> The obvious keyword choices seem to be "nucleic" and "protein". However, this would likely introduce conflicts with existing workflows where e.g. files are named "nucleic.pdb" or "protein.pdb", and PyMOL would load them as named objects of the same name.
> 
> We are looking for new keywords that minimize the chance of such naming conflicts.
> 
> For an overview of the current selection language, see
> https://pymolwiki.org/index.php/Selection_Algebra

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Martin,

Check out this script:
https://pymolwiki.org/index.php/Save_settings

Cheers,
  Thomas

> On Feb 7, 2018, at 12:09 PM, MARTIN ALCORLO PAGES <mal...@iq...> wrote:
> 
> Hi there!
> 
> I am Martin, I would like to know if there is a way to export the settings from a particular Pymol session to another different session.
> 
> Thanks very much in advance!!

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi there!

I am Martin, I would like to know if there is a way to export the  
settings from a particular Pymol session to another different session.

Thanks very much in advance!!

Hi Murpholino,

You could convert your volume colors to a ramp object with a Python script like this:

# conversion function
def volume2ramp(volname, rampname='', mapname='none'):
    v = cmd.volume_color(volname)
    colors = []
    for i in range(0, len(v), 5):
        colors.append('0x%02x%02x%02x' % (
                    int(v[i + 1] * 0xff),
                    int(v[i + 2] * 0xff),
                    int(v[i + 3] * 0xff)))
    cmd.ramp_new(rampname or cmd.get_unused_name('ramp'),
            mapname, v[0::5], colors)

# apply to your volume object
volume2ramp('myvolume')

Hope that helps.

Cheers,
  Thomas

> On Feb 6, 2018, at 3:36 PM, Murpholino Peligro <mur...@gm...> wrote:
> 
> Is there a way to add a color bar to a volume?
> I am looking for something like the bar in the last picture here (https://pymolwiki.org/index.php/Ramp_New)
> This is my volume https://www.dropbox.com/s/x4ic7uvdlknk8us/volume.png?dl=0
> 
> 
> Thanks. 

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

The PyMOL team has an open position for a software engineer!

We are looking for a highly qualified software engineer and would love to fill this position from within the community. The ideal candidate has a background in computational chemistry or biology and is an avid PyMOL users. Ability to write C++ and Python code that is well-designed, modular, maintainable, testable, and documented is essential.

PyMOL has an amazing user base and your contribution will have a recognized impact.

Details and how to apply:
https://www.schrodinger.com/careers/software-engineers/3d-scientific-visualization-software-engineer-0

Cheers,
  The PyMOL Team at Schrödinger

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Is there a way to add a color bar to a volume?
I am looking for something like the bar in the last picture here (
https://pymolwiki.org/index.php/Ramp_New)
This is my volume https://www.dropbox.com/s/x4ic7uvdlknk8us/volume.png?dl=0


Thanks.

Dear PyMOL users,

I would like to combine two pymol sessions together to compare to different conformations of a molecule that I have in two different pse files.

One of you suggested me the following (and this works with others)

load session1.pse
load session2.pse, partial=1

but in my case, when I open a new pymol session and type : load nameofmysession.pse I get an error saying 'can't open  nameofmysession.pse' ? Is this because pymol doesn't find my pse  file in my computer ? If yes, where should I store my pse session files ?

Also, regarding how to proceed: Should I open a new pymol session and type the two command lines above successively ? For example, should I type "load session1.pse" first, hit enter and then type 'load session2.pse, partial=1' ??

Many thanks for your help,

Maria

Hello pymol-users, fyi ...

25th Annual Tcl/Tk Conference (Tcl'2018)
http://www.tcl.tk/community/tcl2018/

October 15 - 19, 2018
Crowne Plaza Houston River Oaks
2712 Southwest Freeway, 77098
Houston, Texas, USA

Important Dates:

Abstracts and proposals due   August 20, 2018
Notification to authors       August 27, 2018
WIP and BOF reservations open July 23, 2018     ** may change **
Registration opens            August 20, 2018     ** may change **
Author materials due          September 24, 2018
Tutorials Start               October 15, 2018
Conference starts             October 17, 2018

Email Contact:                tcl...@go...

Submission of Summaries

Tcl/Tk 2018 will be held in Houston, Texas, USA from October 15, 2018 to October 19, 2018.

The program committee is asking for papers and presentation proposals
from anyone using or developing with Tcl/Tk (and extensions). Past
conferences (Proceedings: http://www.tcl.tk/community/conferences.html)
have seen submissions covering a wide variety of topics including:

* Scientific and engineering applications
* Industrial controls
* Distributed applications and Network Managment
* Object oriented extensions to Tcl/Tk
* New widgets for Tk
* Simulation and application steering with Tcl/Tk
* Tcl/Tk-centric operating environments
* Tcl/Tk on small and embedded devices
* Medical applications and visualization
* Use of different programming paradigms in Tcl/Tk and proposals for new
  directions.
* New areas of exploration for the Tcl/Tk language

Submissions should consist of an abstract of about 100 words and a
summary of not more than two pages, and should be sent as plain text
to tcl...@go... no later than August 20, 2018. Authors of accepted
abstracts will have until September 24, 2018 to submit their final
paper for the inclusion in the conference proceedings. The proceedings
will be made available on digital media, so extra materials such as
presentation slides, code examples, code for extensions etc. are
encouraged.

Printed proceedings will be produced as an on-demand book at lulu.com
Online proceedings will appear via
	http://www.tcl.tk/community/conferences.html

The authors will have 30 minutes to present their paper at
the conference.

The program committee will review and evaluate papers according to the
following criteria:

* Quantity and quality of novel content
* Relevance and interest to the Tcl/Tk community
* Suitability of content for presentation at the conference

Proposals may report on commercial or non-commercial systems, but
those with only blatant marketing content will not be accepted.

Application and experience papers need to strike a balance between
background on the application domain and the relevance of Tcl/Tk to
the application. Application and experience papers should clearly
explain how the application or experience illustrates a novel use of
Tcl/Tk, and what lessons the Tcl/Tk community can derive from the
application or experience to apply to their own development efforts.

Papers accompanied by non-disclosure agreements will be returned to
the author(s) unread. All submissions are held in the highest
confidentiality prior to publication in the Proceedings, both as a
matter of policy and in accord with the U. S. Copyright Act of 1976.

The primary author for each accepted paper will receive registration
to the Technical Sessions portion of the conference at a reduced rate.

Other Forms of Participation

The program committee also welcomes proposals for panel discussions of
up to 90 minutes. Proposals should include a list of confirmed
panelists, a title and format, and a panel description with position
statements from each panelist. Panels should have no more than four
speakers, including the panel moderator, and should allow time for
substantial interaction with attendees. Panels are not presentations
of related research papers.

Slots for Works-in-Progress (WIP) presentations and Birds-of-a-Feather
sessions (BOFs) are available on a first-come, first-served basis
starting in July 23, 2018. Specific instructions for reserving WIP
and BOF time slots will be provided in the registration information
available in July 23, 2018. Some WIP and BOF time slots will be held open
for on-site reservation. All attendees with an interesting work in
progress should consider reserving a WIP slot.

Registration Information

More information on the conference is available the conference Web
site (http://www.tcl.tk/community/tcl2018/) and will be published on
various Tcl/Tk-related information channels.

To keep in touch with news regarding the conference, subscribe to the
tcl...@go... list. See:
https://groups.google.com/forum/#!forum/tclconference for list
information, archive, and subscription.

To keep in touch with Tcl events in general, subscribe to the
tcl-announce list. See: http://code.activestate.com/lists/tcl-announce
for list information, archive, and subscription.

Conference Committee

   * Alexandre Ferrieux
   * Andreas Kupries
   * Arjen Markus       Deltares
   * Brian Griffin      Mentor - A Siemens Business
   * Clif Flynt         Noumena Corp
   * Gerald Lester      RubyLane
   * Joe Mistachkin     Mistachkin Systems
   * Ronald Fox         CAEN Technologies
                        NSCL @ Michigan State University
   * Steve Landers      Digital Smarties

Contact Information     tcl...@go...

Tcl'2018 would like to thank those who are sponsoring the conference:

   * ActiveState Inc
   * FlightAware
   * Mentor - A Siemens Business
   * Noumena Corp
   * Tcl Community Association

Hi Ahmad, there are a number of pymol tutorials online that should be
helpful. From the first page of a Google search, some that look helpful
include:
https://www.mrc-lmb.cam.ac.uk/rlw/text/MacPyMOL_tutorial.html
https://bioquest.org/nimbios2010/wp-content/blogs.dir/files/2010/07/pymol_tutorial3.pdf
https://www.youtube.com/watch?v=1cIE9owcy2s

Hope this helps

On Sun, Feb 4, 2018 at 9:39 AM, Ahmad Abdelzaher <und...@gm...>
wrote:

> Hello,
>
> Is there a way to keep the sequence of structure, but remove the modelling
> of some flexible loop? Meaning, Pymol should show the entire sequence, but
> the strcuture should not show this sequence.
>
> A side question, how else can I compare two structures in Pymol besides
> aligning them and comparing RMSD?
>
> Regards.
>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi!

This is my first e-mail to this list. Sorry in advance for my bad english.

I've been using APBS for the past month in order to build protein binding
sites representations for a artificial neural network I've been working on.
At first I used the OpenDX output file from APBS stand-alone but I wanted
to generate Isomesh files aswell, in order to store the files conveniently
for future analysis or even to use as data input at some order work.

1- When APBS finished calculation, it creates a map object. But how does
PyMol translate the .dx map into that beautiful Isomesh? (achievable using
the Isomesh command aswell)

2- How to save that isomesh in a way I could open it again with Pymol or
another Visualization tool? (I already tried saving as .wrl. but I cannot
open it on Pymol and the file syntax is confusing)

3- Are there any other softwares or libraries to do such things? (output
isomesh at one specific level (5), store it in a convenient way, etc)

Thanks for the attention.

-- 
Fernando Limoeiro Lara de Oliveira, Graduando, Biofísica - UFRJ - Xerém
Aluno de Iniciação Científica
Laboratório de Biologia Computacional - LaBiC
Diretório de Metrologia Aplicada às Ciências da Vida - DIMAV
Instituto Nacional de Metrologia, Qualidade e Tecnologia - INMETRO
Av. Nossa Senhora das Graças, 50 - Xerém, Duque de Caxias, RJ - CEP:
25250-020
Tel.: +55 21 2145-3070
Lattes *curriculum*: http://lattes.cnpq.br/5677811257298963

Hello,

Is there a way to keep the sequence of structure, but remove the modelling
of some flexible loop? Meaning, Pymol should show the entire sequence, but
the strcuture should not show this sequence.

A side question, how else can I compare two structures in Pymol besides
aligning them and comparing RMSD?

Regards.

Thanks a lot. I am using windows 7 and windows 10. It's obviously no big
deal, just a minor annoyance ;-)
Gary


On 1 February 2018 at 11:57, Thomas Holder <tho...@sc...>
wrote:

> Hi Gary,
>
> Which operating system do you use?
>
> PyMOL 1.x was hard coded to place the window in the upper left corner of
> the screen. PyMOL 2.x leaves window placement up to the operating system
> (window manager). E.g. KDE on Linux places the window in the least occupied
> screen area (my favorite), MacOS always puts it in the center of the screen.
>
> If you're launching from the command line, you could also specify width
> and height like this, which is applied before the window manager places the
> window:
> pymol -W 1350 -H 950
>
> PyMOL 2.1 will bring back the "window" command (it's non-functional in
> 2.0), which hopefully will resolve the issue for you. It will allow you to
> fit the window back onto the screen after resizing.
>
> # pymolrc:
> cmd.viewport(1350, 950)
> cmd.window('fit')
>
> A pre-release build of PyMOL 2.1 is available here:
> https://pymol.org/alpha/
>
> Cheers,
>   Thomas
>
> > On Jan 31, 2018, at 9:58 AM, Gary Hunter <gar...@um...> wrote:
> >
> > My pymolrc file contains a line: viewport 1350,950
> > which nicely fills my screen when I start pymol 1.8. However in pymol2
> the screen has the correct dimensions but the whole thing is offest to the
> right and down. What should be the top left corner of the window is placed
> about a quarter of the way from the left hand side and about one sixth of
> the way down from the top.
> >
> > Is it a bug or is there a new viewport command?
> >
> >
> >
> > --
> > Prof. Gary J. Hunter,
> >
> > Laboratory of Biochemistry and Protein Science,
> >
> > Department of Physiology and Biochemistry,
> >
> > University of Malta, Msida, MSD 2080, Malta.
> >
> > phone: +356 2340 2917
> >
> > phone: +356 21316655 (secretary),  Fax: +356 21310577
> >
> > http://www.um.edu.mt/ms/physbiochem
> >
> > There may be confidential information within the contents of this email
> meant only for the person addressed. This email must not be forwarded to
> third parties without the express consent of the sender. If you believe you
> have received this email in error please inform the sender and remove it
> from your system.
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>


-- 

Prof. Gary J. Hunter,

Laboratory of Biochemistry and Protein Science,

Department of Physiology and Biochemistry,

University of Malta, Msida, MSD 2080, Malta.

phone: +356 2340 2917

phone: +356 21316655 (secretary),  Fax: +356 21310577

http://www.um.edu.mt/ms/physbiochem

There may be confidential information within the contents of this email
meant only for the person addressed. This email must not be forwarded to
third parties without the express consent of the sender. If you believe you
have received this email in error please inform the sender and remove it
from your system.

Hi Gary,

Which operating system do you use?

PyMOL 1.x was hard coded to place the window in the upper left corner of the screen. PyMOL 2.x leaves window placement up to the operating system (window manager). E.g. KDE on Linux places the window in the least occupied screen area (my favorite), MacOS always puts it in the center of the screen.

If you're launching from the command line, you could also specify width and height like this, which is applied before the window manager places the window:
pymol -W 1350 -H 950

PyMOL 2.1 will bring back the "window" command (it's non-functional in 2.0), which hopefully will resolve the issue for you. It will allow you to fit the window back onto the screen after resizing.

# pymolrc:
cmd.viewport(1350, 950)
cmd.window('fit')

A pre-release build of PyMOL 2.1 is available here: https://pymol.org/alpha/

Cheers,
  Thomas

> On Jan 31, 2018, at 9:58 AM, Gary Hunter <gar...@um...> wrote:
> 
> My pymolrc file contains a line: viewport 1350,950
> which nicely fills my screen when I start pymol 1.8. However in pymol2 the screen has the correct dimensions but the whole thing is offest to the right and down. What should be the top left corner of the window is placed about a quarter of the way from the left hand side and about one sixth of the way down from the top.
> 
> Is it a bug or is there a new viewport command?
> 
> 
> 
> -- 
> Prof. Gary J. Hunter,
> 
> Laboratory of Biochemistry and Protein Science,
> 
> Department of Physiology and Biochemistry,
> 
> University of Malta, Msida, MSD 2080, Malta.
> 
> phone: +356 2340 2917
> 
> phone: +356 21316655 (secretary),  Fax: +356 21310577
> 
> http://www.um.edu.mt/ms/physbiochem
> 
> There may be confidential information within the contents of this email meant only for the person addressed. This email must not be forwarded to third parties without the express consent of the sender. If you believe you have received this email in error please inform the sender and remove it from your system.

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Vijay,

All "by"-operators have a weak priority, so you'll need an extra set of parenthesis there:

carb_pos = cmd.select('e. C and (byring e. C) and (pc.>0)')

See also the yellow highlighted note about "Entity expansion" here:
https://pymolwiki.org/index.php/Selection_Algebra

Cheers,
  Thomas

> On Feb 1, 2018, at 4:16 AM, Vijay Masand <vij...@gm...> wrote:
> 
> Dear PyMOL users,
> Today, I used following command to select positively charged ring
> carbon atoms, surprisingly, PyMOL 2.0.7 selected negatively charged
> ring carbon atoms also. Is it a bug or issue associated with 'Byring'?
> carb_pos = cmd.select('e. C and Byring e. C and (pc.>0)')
> I am sharing the image for better understanding.
> Cheers
> Vijay

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear PyMOL users,
Today, I used following command to select positively charged ring
carbon atoms, surprisingly, PyMOL 2.0.7 selected negatively charged
ring carbon atoms also. Is it a bug or issue associated with 'Byring'?
carb_pos = cmd.select('e. C and Byring e. C and (pc.>0)')
I am sharing the image for better understanding.
Cheers
Vijay

-- 
Assistant Professor
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/