pymol-users Mailing List for PyMOL Molecular Graphics System

Dear PyMOL people,

Please can anyone tell me if there's a standard way to select either of
nucleic / protein separately?

I can use `polymer` to get both together but I can't see a standard way to
distinguish nucleic / protein within that.

I'm currently using something like `resn A+C+G+U+DA+DC+DG+DT` to identify
nucleic but that's inadequate because it misses out various resn values (eg
BRU, OMG etc) that are part of modified DNA/RNA.

The thing is: PyMOL clearly *knows* which bits are protein versus nucleic
because it draws the cartoons accordingly. So it feels like I should be
accessing this info from PyMOL rather than trying to hack together a list
of resn values.

Many thanks for any help.

Tony Lewis

 
 
 

Hi Lucile,  

 

Sounds like the same problem I had recently (Nvidia 3D graphics were not used for PyMOL, but the built in Intel ones).  

 

Below is Thomas's reply with a link to instructions that fixed it for me.  

 

Cheers, Marko

 
 
On 11/10/2017 12:44, Thomas Holder wrote:
 
>  
>  Hi Marko, Have you seen my reply?  https://sourceforge.net/p/pymol/mailman/message/36070511/  Thomas 

 
 
 
 
 -- Marko Hyvonen Department of Biochemistry, University of Cambridge mh...@ca... +44-(0)1223-766 044 @HyvonenGroup http://hyvonen.bioc.cam.ac.uk 

 
 
 
 
 
>  
> On 25 Nov 2017 at 19:19,  <Lucile Fischer>  wrote:
>  
>  
>  Hi, I have some trouble with the Pymol viewer window which is somehow cut on the sides (see image) unless I display it as Fullscreen. This problem prevents to use a protein sequence for example as it does not appear on screen. Do you have any idea of why is this happening ? thanks Lucile Fischer 
>  
>  
>  
>  
>  ------------------------------------------------------------------------------ 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,

I have some trouble with the Pymol viewer window which is somehow cut on 
the sides (see image) unless I display it as Fullscreen. This problem 
prevents to use a protein sequence for example as it does not appear on 
screen. Do you have any idea of why is this happening ?

thanks

Lucile Fischer

OK,
I found the answer myself, googling in this email list. Sources will be 
released early next year, I understood. I'll wait patiently :)

Cheers,
Albert

On 22/11/17 11:49, Albert Solernou wrote:
> Dear All,
> we have been writing a plugin for PyMOL during the last years, released 
> as GPL. I would like to support PyMOL2, but need to know whether the 
> code will be made accessible or not. Is PyMOL2 still free software? And 
> if so, can we get access to the source code?
> 
> Thanks,
> Albert
> 

-- 
---------------------------------
   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451

Dear All,
we have been writing a plugin for PyMOL during the last years, released 
as GPL. I would like to support PyMOL2, but need to know whether the 
code will be made accessible or not. Is PyMOL2 still free software? And 
if so, can we get access to the source code?

Thanks,
Albert

-- 
---------------------------------
   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451

Hi there,

I wrote a script to pairfit all chains of one molecule with another
molecule. While pairfit for two chains are good, I see the pairfit doesnot
align the some chains properly to the reference structure. The molecule is
fitted upside-down. Is there a way to correct this? or reorient all the
molecules to some specifics, so that the pair-fitting is properly done?

Thanks,
Subha

-- 
Dr. Subha Kalyaanamoorthy
Post Doctoral Fellow
Faculty of Pharmacy and Pharmaceutical Sciences
University of Alberta
Edmonton, Canada.

Hi Simon,

My example works for me in PyMOL version 1.8.0 and later. Which version do you use?

Thomas

> On Nov 18, 2017, at 3:59 PM, Simon Kit Sang Chu <sim...@gm...> wrote:
> 
> Hi Thomas,
> 
> Thanks for your help! But the NME and ACE are added unattached and randomly in the pdb. I simplified with a dipeptide AA instead. The file is attached here.
> 
> Regards,
> Simon
> 
> 2017-11-18 17:04 GMT+08:00 Thomas Holder <tho...@sc...>:
> Hi Simon,
> 
> I think this is the code you're looking for:
> 
> from pymol import cmd, editor
> cmd.set('retain_order', 0)
> cmd.fab('APAPAPAP')
> editor.attach_amino_acid("last name C", 'nme')
> editor.attach_amino_acid("first name N", 'ace')
> 
> Hope that helps.
> 
> Cheers,
>   Thomas
> 
> > On Nov 17, 2017, at 8:26 AM, Simon Kit Sang Chu <sim...@gm...> wrote:
> >
> > Hi everyone,
> >
> > I am generating segments of peptide to be used in GROMACS. I might be using amber which does not allow automatic capping. Therefore, I hope to solve it with Pymol.
> >
> > Currently, I use a pml scipt to generate the pdb file automatically. The script is simple.
> >
> > for aa in "APAPAPAP" : cmd._alt(string.lower(aa))
> > cmd.save("peptide.pdb")
> >
> > However, if I want to add NME and ACE caps, is there any residue code available? Like XAPAPAPAPY where X and Y are NME and ACE? The main point is to automize the process since I don't want to write NME / ACE manually everytime.
> >
> > I appreciate any suggestion and comment.
> >
> > Regards,
> > Simon
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
> <peptide.pdb>

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Thomas,

Thanks for your help! But the NME and ACE are added unattached and randomly
in the pdb. I simplified with a dipeptide AA instead. The file is attached
here.

Regards,
Simon

2017-11-18 17:04 GMT+08:00 Thomas Holder <tho...@sc...>:

> Hi Simon,
>
> I think this is the code you're looking for:
>
> from pymol import cmd, editor
> cmd.set('retain_order', 0)
> cmd.fab('APAPAPAP')
> editor.attach_amino_acid("last name C", 'nme')
> editor.attach_amino_acid("first name N", 'ace')
>
> Hope that helps.
>
> Cheers,
>   Thomas
>
> > On Nov 17, 2017, at 8:26 AM, Simon Kit Sang Chu <sim...@gm...>
> wrote:
> >
> > Hi everyone,
> >
> > I am generating segments of peptide to be used in GROMACS. I might be
> using amber which does not allow automatic capping. Therefore, I hope to
> solve it with Pymol.
> >
> > Currently, I use a pml scipt to generate the pdb file automatically. The
> script is simple.
> >
> > for aa in "APAPAPAP" : cmd._alt(string.lower(aa))
> > cmd.save("peptide.pdb")
> >
> > However, if I want to add NME and ACE caps, is there any residue code
> available? Like XAPAPAPAPY where X and Y are NME and ACE? The main point is
> to automize the process since I don't want to write NME / ACE manually
> everytime.
> >
> > I appreciate any suggestion and comment.
> >
> > Regards,
> > Simon
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Hi Davinder,

Usually such crashes are related to the graphics driver.

Does PyMOL 2.0 also crash on your machine?
https://pymol.org/2/#download

Thomas

> On Nov 14, 2017, at 11:44 PM, Dhalla, Davinder <d....@ul...> wrote:
> 
> Hi,
> 
> I am trying to launch Pymol version 1.8.7.0. on my CentOS 7 OS.
> Everytime I try to launch it, it crashes with a message:
> /usr/bin/pymol: line 3: 19995 Segmentation fault      (core dumped) "/usr/bin/python" "/usr/lib64/python2.7/site-packages/pymol/__init__.py" "$@"
> 
> What should I do?
> 
> Regards
> Davinder 

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Simon,

I think this is the code you're looking for:

from pymol import cmd, editor
cmd.set('retain_order', 0)
cmd.fab('APAPAPAP')
editor.attach_amino_acid("last name C", 'nme')
editor.attach_amino_acid("first name N", 'ace')

Hope that helps.

Cheers,
  Thomas

> On Nov 17, 2017, at 8:26 AM, Simon Kit Sang Chu <sim...@gm...> wrote:
> 
> Hi everyone,
> 
> I am generating segments of peptide to be used in GROMACS. I might be using amber which does not allow automatic capping. Therefore, I hope to solve it with Pymol.
> 
> Currently, I use a pml scipt to generate the pdb file automatically. The script is simple. 
> 
> for aa in "APAPAPAP" : cmd._alt(string.lower(aa))
> cmd.save("peptide.pdb")
> 
> However, if I want to add NME and ACE caps, is there any residue code available? Like XAPAPAPAPY where X and Y are NME and ACE? The main point is to automize the process since I don't want to write NME / ACE manually everytime.
> 
> I appreciate any suggestion and comment.
> 
> Regards,
> Simon

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi everyone,

I am generating segments of peptide to be used in GROMACS. I might be using
amber which does not allow automatic capping. Therefore, I hope to solve it
with Pymol.

Currently, I use a pml scipt to generate the pdb file automatically. The
script is simple.


for aa in "APAPAPAP" : cmd._alt(string.lower(aa))
cmd.save("peptide.pdb")


However, if I want to add NME and ACE caps, is there any residue code
available? Like *X*APAPAPAP*Y* where X and Y are NME and ACE? The main
point is to automize the process since I don't want to write NME / ACE
manually everytime.

I appreciate any suggestion and comment.

Regards,
Simon

Hi,

I am trying to launch Pymol version 1.8.7.0. on my CentOS 7 OS.
Everytime I try to launch it, it crashes with a message:
/usr/bin/pymol: line 3: 19995 Segmentation fault      (core dumped)
"/usr/bin/python" "/usr/lib64/python2.7/site-packages/pymol/__init__.py"
"$@"

What should I do?

Regards

*Davinder *

Hi Célien,

In my understanding, since every aromatic carbon is sp2 hybridized, PyMOL's output is not wrong. The problem is that PyMOL only knows about delocalized bonds, it doesn't have a proper concept of aromaticity (doesn't implement Hückel's rule). For example you sometimes also see PyMOL's "aromatic" bonds on carboxyl groups.

There is actually some code to classify atoms with delocalized bonds as aromatic for MOL2 output, but it's disabled:
https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer2/Mol2Typing.cpp#l35

Bonds are exported as aromatic (ar) because the MOL2 format doesn't have a "delocalized" type, so "ar" is still the best match for PyMOL's classification.

Hope that helps.

Cheers,
  Thomas

> On Nov 14, 2017, at 12:10 PM, Célien Jacquemard - Employé <jac...@un...> wrote:
> 
> Hello,
> 
> I'm using PyMOL 1.8.6.1 (64 bits) on a Linux distribution (CentOS 7). I used PyMOL API for CE alignment (protein and ligand) with a reference (target) protein. Then, I saved the aligned protein and ligand. Input and output format are mol2. However, I noticed that atomic types from aromatic ring aren't correct. From the input file, type is 'C.ar' but becomes 'C.2' in the output file. The right bond type is conserved (C.ar).
> 
> So my question is: Is it a bug or an expected behavior ?
> 
> Best regards
> 
> Célien Jacquemard

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hello,

I'm using PyMOL 1.8.6.1 (64 bits) on a Linux distribution (CentOS 7). I 
used PyMOL API for CE alignment (protein and ligand) with a reference 
(target) protein. Then, I saved the aligned protein and ligand. Input 
and output format are mol2. However, I noticed that atomic types from 
aromatic ring aren't correct. From the input file, type is 'C.ar' but 
becomes 'C.2' in the output file. The right bond type is conserved (C.ar).

So my question is: Is it a bug or an expected behavior ?

Best regards

Célien Jacquemard

<html>
  <head>

    <meta http-equiv="content-type" content="text/html; charset=windows-1252">
  </head>
  <body bgcolor="#FFFFFF" text="#000000">
    <p><tt>And my reply to the PyMOL list too...</tt><br>
    </p>
    <div class="moz-forward-container"><br>
      -------- Forwarded Message --------
      <table class="moz-email-headers-table" border="0" cellpadding="0"
        cellspacing="0">
        <tbody>
          <tr>
            <th align="RIGHT" nowrap="nowrap" valign="BASELINE">Subject:
            </th>
            <td>Re: [PyMOL] Viewer Window Clipped at Border</td>
          </tr>
          <tr>
            <th align="RIGHT" nowrap="nowrap" valign="BASELINE">Date: </th>
            <td>Wed, 8 Nov 2017 14:50:36 +0000</td>
          </tr>
          <tr>
            <th align="RIGHT" nowrap="nowrap" valign="BASELINE">From: </th>
            <td>Marko Hyvonen <a class="moz-txt-link-rfc2396E" href="mailto:mh...@ca...">&lt;mh...@ca...&gt;</a></td>
          </tr>
          <tr>
            <th align="RIGHT" nowrap="nowrap" valign="BASELINE">To: </th>
            <td>Nicholas Fitzkee <a class="moz-txt-link-rfc2396E" href="mailto:nfi...@gm...">&lt;nfi...@gm...&gt;</a></td>
          </tr>
        </tbody>
      </table>
      <br>
      <br>
      <meta content="text/html; charset=windows-1252"
        http-equiv="Content-Type">
      <p>Sounds like the same problem I had recently (Nvidia graphics
        not used for PyMOL, but the built in Intel ones). <br>
      </p>
      <p>Below is Thomas's reply with a link to instructions that fixed
        it for me!</p>
      <p>Cheers, Marko<br>
      </p>
      <br>
      <div class="moz-cite-prefix">On 11/10/2017 12:44, Thomas Holder
        wrote:<br>
      </div>
      <blockquote
        cite="mid:914...@sc..."
        type="cite">
        <pre wrap="">Hi Marko,

Have you seen my reply?
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="https://sourceforge.net/p/pymol/mailman/message/36070511/" rel="nofollow">https://sourceforge.net/p/pymol/mailman/message/36070511/">https://sourceforge.net/p/pymol/mailman/message/36070511/</a>

Thomas</pre>
      </blockquote>
      <br>
      <div class="moz-cite-prefix">On 08/11/2017 14:46, Nicholas Fitzkee
        wrote:<br>
      </div>
      <blockquote
cite="mid:CAB...@ma..."
        type="cite">
        <div dir="ltr">
          <div>
            <div>
              <div>
                <div>
                  <div>
                    <div>
                      <div>
                        <div>Hi all,<br>
                          <br>
                        </div>
                        I'm using PyMOL 1.8.6.1 on Windows 10 x64, and
                        with the recent versions on my system, the
                        viewer window is clipped around the border. In
                        the object list, only the lower half of the
                        object's name is displayed, and in the viewer
                        command line, only the upper half of the text is
                        displayed. Even at the right and left border, I
                        notice that text within the viewer window is
                        being cut off.  It's as if the window size is
                        too small for what is being rendered in the
                        viewer window.<br>
                      </div>
                      <div><br>
                      </div>
                      <div>This seems to affect the mouse position as
                        well, because there seems to be an offset
                        between my mouse position and the click location
                        when I select buttons in the object list.<br>
                      </div>
                      <div><br>
                      </div>
                      I've posted an example on my website:<br>
                      <a moz-do-not-send="true"
href="http://fitzkee.chemistry.msstate.edu/dropbox/pymol_capture_20171108.png
" rel="nofollow">http://fitzkee.chemistry.msstate.edu/dropbox/pymol_capture_20171108.png">http://fitzkee.chemistry.msstate.edu/dropbox/pymol_capture_20171108.png</a><br>
                      <br>
                    </div>
                    Note how the object list and command line are not
                    fully shown. Resizing the window does not remedy
                    this problem.<br>
                    <br>
                  </div>
                  This isn't just a problem with Open Source PyMOL; the
                  recent educational versions from Schrodinger have the
                  same problem. PyMOL 0.99 works fine.<br>
                  <br>
                </div>
                PyMOL startup is below.<br>
                <br>
              </div>
              Thanks for any help,<br>
            </div>
            Nick<br>
            <br>
          </div>
          --- snip ---<br>
          <br>
           PyMOL(TM) Molecular Graphics System, Version 1.8.6.1.<br>
           Copyright (c) Schrodinger, LLC.<br>
           All Rights Reserved.<br>
           <br>
              Created by Warren L. DeLano, Ph.D. <br>
           <br>
              PyMOL is user-supported open-source software.  Although
          some versions<br>
              are freely available, PyMOL is not in the public domain.<br>
           <br>
              If PyMOL is helpful in your work or study, then please
          volunteer <br>
              support for our ongoing efforts to create open and
          affordable scientific<br>
              software by purchasing a PyMOL Maintenance and/or Support
          subscription.<br>
           <br>
              More information can be found at "<a
            moz-do-not-send="true" href="http://www.pymol.org">http://www.pymol.org</a>".<br>
           <br>
              Enter "help" for a list of commands.<br>
              Enter "help &lt;command-name&gt;" for information on a
          specific command.<br>
           <br>
           Hit ESC anytime to toggle between text and graphics.<br>
           <br>
           Detected OpenGL version 2.0 or greater. Shaders available.<br>
           Detected GLSL version 4.40.<br>
           OpenGL graphics engine:<br>
            GL_VENDOR:   Intel<br>
            GL_RENDERER: Intel(R) HD Graphics 530<br>
            GL_VERSION:  4.4.0 - Build 21.20.16.4664<br>
           Detected 8 CPU cores.  Enabled multithreaded rendering.<br>
           OpenGL quad-buffer stereo 3D detected and enabled.<br>
        </div>
        <br>
        <fieldset class="mimeAttachmentHeader"></fieldset>
        <br>
        <pre wrap="">------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://sdm.link/slashdot

Hi all,

I'm using PyMOL 1.8.6.1 on Windows 10 x64, and with the recent versions on
my system, the viewer window is clipped around the border. In the object
list, only the lower half of the object's name is displayed, and in the
viewer command line, only the upper half of the text is displayed. Even at
the right and left border, I notice that text within the viewer window is
being cut off.  It's as if the window size is too small for what is being
rendered in the viewer window.

This seems to affect the mouse position as well, because there seems to be
an offset between my mouse position and the click location when I select
buttons in the object list.

I've posted an example on my website:
http://fitzkee.chemistry.msstate.edu/dropbox/pymol_capture_20171108.png

Note how the object list and command line are not fully shown. Resizing the
window does not remedy this problem.

This isn't just a problem with Open Source PyMOL; the recent educational
versions from Schrodinger have the same problem. PyMOL 0.99 works fine.

PyMOL startup is below.

Thanks for any help,
Nick

--- snip ---

 PyMOL(TM) Molecular Graphics System, Version 1.8.6.1.
 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 <command-name>" for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 4.40.
 OpenGL graphics engine:
  GL_VENDOR:   Intel
  GL_RENDERER: Intel(R) HD Graphics 530
  GL_VERSION:  4.4.0 - Build 21.20.16.4664
 Detected 8 CPU cores.  Enabled multithreaded rendering.
 OpenGL quad-buffer stereo 3D detected and enabled.

Thank you. I didn't notice there's a Pymol 2 out already. I will definitely
download it.

Trying chmod +x setup.sh then ./setup.sh gives:

======================================================================
Running setup.sh no longer creates a wrapper script unless you provide
an output filename (./setup.sh /path/to/pymolwrapper). We recommend to
just use the existing "pymol" launch script from this directory. You
may want to create a symlink in $PATH, for example:
ln -s $PWD/pymol /usr/local/bin/
======================================================================

======================================================================
Checking if any library from "ext/libextra" is required on this system
======================================================================

Launching like this ./pymol does work. I wonder how to create a desktop
icon for it though. Thank you.

On Mon, Nov 6, 2017 at 6:56 AM, Thomas Holder <tho...@sc...
> wrote:

> Hi Ahmad,
>
> Inside the pymol directory, run:
>
> ./pymol
>
> In case the external window does not open, install the LibXScrnSaver
> package on your system.
>
> Is there a reason why you don't use PyMOL 2.0 instead? We do provide an
> edu license file for PyMOL 2.0 on the Edu PyMOL download page.
>
> Cheers,
>   Thomas
>
> > On Nov 5, 2017, at 11:49 PM, Ahmad Abdelzaher <und...@gm...>
> wrote:
> >
> > I just downloaded the free Edupymol version, EduPyMOL-v1.7.4.5-Linux-x86_
> 64.tar.bz2.
> >
> > I untarred using tar -xvjf  EduPyMOL-v1.7.4.5-Linux-x86_64.tar.bz2.
> >
> > Now I have a folder called pymol with the following files / directories:
> >
> > data  examples  ext  modules  pymol  pymol.exe  scripts  setup.sh
> >
> > How should I install and run it?
> >
> > Regards.
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Hi Ahmad,

Inside the pymol directory, run:

./pymol

In case the external window does not open, install the LibXScrnSaver package on your system.

Is there a reason why you don't use PyMOL 2.0 instead? We do provide an edu license file for PyMOL 2.0 on the Edu PyMOL download page.

Cheers,
  Thomas

> On Nov 5, 2017, at 11:49 PM, Ahmad Abdelzaher <und...@gm...> wrote:
> 
> I just downloaded the free Edupymol version, EduPyMOL-v1.7.4.5-Linux-x86_64.tar.bz2.
> 
> I untarred using tar -xvjf  EduPyMOL-v1.7.4.5-Linux-x86_64.tar.bz2.
> 
> Now I have a folder called pymol with the following files / directories:
> 
> data  examples  ext  modules  pymol  pymol.exe  scripts  setup.sh
> 
> How should I install and run it?
> 
> Regards.

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

I just downloaded the free Edupymol
version, EduPyMOL-v1.7.4.5-Linux-x86_64.tar.bz2.

I untarred using tar -xvjf  EduPyMOL-v1.7.4.5-Linux-x86_64.tar.bz2.

Now I have a folder called pymol with the following files / directories:

data  examples  ext  modules  pymol  pymol.exe  scripts  setup.sh


How should I install and run it?


Regards.

Hi Thomas,

Many thanks.

Best,

Li

On Thu, Nov 2, 2017 at 2:39 PM, Thomas Holder <tho...@sc...
> wrote:

> Hi Li,
>
> Showing sticks:
> show sticks, b > 20 and b < 50
>
> Iterating over residues:
> iterate byca (b > 20 and b < 50), print(resi)
>
> Cheers,
>   Thomas
>
> > On Nov 1, 2017, at 6:18 PM, Li Xue <me....@gm...> wrote:
> >
> > Hello,
> >
> > I want to select residues with a specific range of b-factor values, and
> show stricks for them. How can I use commands to do it?
> >
> > Many thanks.
> >
> > Li
> >
> > --
> > Li Xue, Ph.D.
> > Computational Structural Biology group
> > Utrecht University, Faculty of Science - Chemistry
> > Email: L....@uu...
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>


-- 
Li Xue, Ph.D.
Computational Structural Biology group
Utrecht University, Faculty of Science - Chemistry
Email: L....@uu...

Hi Simon,

zSpace support was never in any official PyMOL release (neither Open-Source nor Incentive PyMOL).

The zSpace company had their own custom patched version of Open-Source PyMOL which they deployed to some customers. I don't know if they still support it.

Cheers,
  Thomas

> On Oct 25, 2017, at 2:26 PM, Su, Simon M CIV USARMY RDECOM ARL (US) <sim...@ma...> wrote:
> 
> CLASSIFICATION: UNCLASSIFIED
> 
> Hello,
> 
> While googling for "zspace molecular visualization", I came across
> http://zspace.com/about/press-releases/zspace-announces-platform-support-for
> -pymol-and-avogadro released back in 2013. However, when I tried to google
> for information on how to run either PyMOL or Avogadro on zSpace, I am not
> able to find anything useful. 
> 
> Is the support for zSpace in PyMOL not available in the open source version?
> If it is supported, where can I find more information on getting that setup?
> 
> 
> Any pointers in greatly appreciated.... Thank you....
> 
> thanks
> -simon
> 
> 
> CLASSIFICATION: UNCLASSIFIED

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Verena,

You're not doing anything wrong. Generation of .mtl output is not implemented.

Of course saving an empty file is useless and confusing. We should remove the (non-functional) .mtl export and raise a warning if someone tries to save an .mtl file.

Cheers,
  Thomas

> On Oct 26, 2017, at 4:02 PM, Verena Resch <ver...@gm...> wrote:
> 
> Hi all,
> I was wondering if there is an option to export both the .obj and .mtl file from pymol.
> Saving as .obj works perfectly fine, however when I save as .mtl the file is empty.
> 
> Am I doing something wrong here?
> I saved via command line „save filename.mtl“
> 
> Would there be another option that the mtl-file is generated automatically during saving as .obj.
> 
> Thanks in advance for the help!
> 
> Verena

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Li,

Showing sticks:
show sticks, b > 20 and b < 50

Iterating over residues:
iterate byca (b > 20 and b < 50), print(resi)

Cheers,
  Thomas

> On Nov 1, 2017, at 6:18 PM, Li Xue <me....@gm...> wrote:
> 
> Hello,
> 
> I want to select residues with a specific range of b-factor values, and show stricks for them. How can I use commands to do it? 
> 
> Many thanks.
> 
> Li
> 
> -- 
> Li Xue, Ph.D.
> Computational Structural Biology group
> Utrecht University, Faculty of Science - Chemistry
> Email: L....@uu...

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Hari - 

The `cartoon_gap_cutoff` setting does this.  https://pymolwiki.org/index.php/Cartoon_gap_cutoff

Cheers,
Jared

On November 2, 2017 at 6:04:12 AM, hari jayaram (ha...@gm...) wrote:

Hi ,
One of the features I like in Chimera is that breaks in the protein chain due to unresolved residues are indicated by dashes.
Is there a plugin or built in feature that enables this in pymol.

Thanks
Hari

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Hello,

I want to select residues with a specific range of b-factor values, and
show stricks for them. How can I use commands to do it?

Many thanks.

Li


-- 
Li Xue, Ph.D.
Computational Structural Biology group
Utrecht University, Faculty of Science - Chemistry
Email: L....@uu...