pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] counting number of standard amino acids in PDB

[James S. <jms...@gm...>]

Dear Pymol Users,

that is not very related to pymol question but however probably it can
be solved via pymol as well ;-)

I am looking for some script (e.g. via running in pymol no-gui), which
will count the number of standard amino acid residues in the given
PDB. E.g. for particular pdb consisted of 9 residues complexed with
part of the ligand I need to print the value of 9 (the end value of
6th column before TER)

ATOM      1  N   MET A   1      24.950   5.224  -5.601  1.00 30.01           N
ATOM      2  CA  MET A   1      24.822   3.740  -5.655  1.00 30.25           C
ATOM      3  C   MET A   1      23.719   3.091  -4.771  1.00 28.98           C
ATOM      4  O   MET A   1      23.417   1.937  -4.989  1.00 28.27           O
ATOM      5  CB  MET A   1      26.187   3.043  -5.448  1.00 31.03           C
ATOM      6  CG  MET A   1      26.869   3.182  -4.084  1.00 32.21           C
ATOM      7  SD  MET A   1      28.713   3.095  -4.227  1.00 34.63           S
ATOM      8  CE  MET A   1      29.205   3.597  -2.564  1.00 33.32           C
ATOM      9  N   LYS A   2      23.111   3.804  -3.818  1.00 27.78           N
ATOM     10  CA  LYS A   2      21.869   3.310  -3.188  1.00 27.21           C
ATOM     11  C   LYS A   2      20.671   4.237  -3.440  1.00 26.27           C
ATOM     12  O   LYS A   2      20.787   5.445  -3.300  1.00 25.96           O
ATOM     13  CB  LYS A   2      22.027   3.091  -1.684  1.00 27.32           C
ATOM     14  CG  LYS A   2      20.820   2.362  -1.065  1.00 27.75           C
ATOM     15  CD  LYS A   2      20.953   2.147   0.439  1.00 28.18           C
ATOM     16  CE  LYS A   2      19.928   1.130   0.938  1.00 29.30           C
ATOM     17  NZ  LYS A   2      20.083   0.809   2.386  1.00 30.36           N1+
ATOM     18  N   PHE A   3      19.528   3.658  -3.808  1.00 24.92           N
ATOM     19  CA  PHE A   3      18.306   4.421  -4.054  1.00 24.39           C
ATOM     20  C   PHE A   3      17.161   3.823  -3.246  1.00 24.12           C
ATOM     21  O   PHE A   3      16.991   2.597  -3.202  1.00 23.77           O
ATOM     22  CB  PHE A   3      17.940   4.222  -5.535  1.00 23.83           C
ATOM     23  CG  PHE A   3      19.003   4.968  -6.434  1.00 23.81           C
ATOM     24  CD1 PHE A   3      19.132   6.337  -6.585  1.00 23.27           C
ATOM     25  CD2 PHE A   3      19.876   4.135  -7.129  1.00 23.46           C
ATOM     26  CE1 PHE A   3      20.110   6.868  -7.412  1.00 23.22           C
ATOM     27  CE2 PHE A   3      20.862   4.660  -7.952  1.00 23.19           C
ATOM     28  CZ  PHE A   3      20.975   6.027  -8.102  1.00 23.07           C
ATOM     29  N   THR A   4      16.374   4.691  -2.624  1.00 23.47           N
ATOM     30  CA  THR A   4      15.326   4.278  -1.704  1.00 23.33           C
ATOM     31  C   THR A   4      13.946   4.720  -2.188  1.00 22.67           C
ATOM     32  O   THR A   4      13.779   5.810  -2.726  1.00 22.24           O
ATOM     33  CB  THR A   4      15.584   4.875  -0.295  1.00 23.52           C
ATOM     34  CG2 THR A   4      14.441   4.560   0.650  1.00 23.80           C
ATOM     35  OG1 THR A   4      16.798   4.328   0.245  1.00 23.98           O
ATOM     36  N   VAL A   5      12.955   3.866  -1.980  1.00 22.25           N
ATOM     37  CA  VAL A   5      11.577   4.216  -2.276  1.00 22.46           C
ATOM     38  C   VAL A   5      10.685   4.011  -1.038  1.00 22.44           C
ATOM     39  O   VAL A   5      10.951   3.145  -0.201  1.00 21.37           O
ATOM     40  CB  VAL A   5      11.033   3.456  -3.533  1.00 21.81           C
ATOM     41  CG1 VAL A   5      11.786   3.902  -4.782  1.00 20.47           C
ATOM     42  CG2 VAL A   5      11.127   1.940  -3.368  1.00 21.55           C
ATOM     43  N   GLY A   6       9.660   4.845  -0.908  1.00 23.27           N
ATOM     44  CA  GLY A   6       8.676   4.684   0.154  1.00 24.59           C
ATOM     45  C   GLY A   6       8.727   5.731   1.249  1.00 25.69           C
ATOM     46  O   GLY A   6       7.834   5.767   2.101  1.00 26.30           O
ATOM     47  N   ASN A   7       9.764   6.568   1.261  1.00 26.66           N
ATOM     48  CA  ASN A   7       9.775   7.728   2.155  1.00 27.39           C
ATOM     49  C   ASN A   7      10.165   9.028   1.436  1.00 27.80           C
ATOM     50  O   ASN A   7      11.263   9.569   1.622  1.00 28.37           O
ATOM     51  CB  ASN A   7      10.619   7.470   3.421  1.00 28.21           C
ATOM     52  CG  ASN A   7      12.089   7.278   3.127  1.00 29.85           C
ATOM     53  ND2 ASN A   7      12.938   7.964   3.897  1.00 32.41           N
ATOM     54  OD1 ASN A   7      12.466   6.525   2.229  1.00 32.61           O
ATOM     55  N   GLY A   8       9.232   9.521   0.622  1.00 27.41           N
ATOM     56  CA  GLY A   8       9.422  10.752  -0.139  1.00 27.40           C
ATOM     57  C   GLY A   8       9.309  10.498  -1.629  1.00 27.35           C
ATOM     58  O   GLY A   8       8.449  11.071  -2.303  1.00 27.93           O
ATOM     59  N   GLN A   9      10.178   9.630  -2.136  1.00 26.80           N
ATOM     60  CA  GLN A   9      10.215   9.294  -3.552  1.00 26.37           C
ATOM     61  C   GLN A   9       9.834   7.833  -3.736  1.00 25.75           C
ATOM     62  O   GLN A   9      10.308   6.970  -2.997  1.00 25.25           O
ATOM     63  CB  GLN A   9      11.622   9.522  -4.115  1.00 26.74           C
ATOM     64  CG  GLN A   9      12.197  10.924  -3.899  1.00 27.40           C
ATOM     65  CD  GLN A   9      11.327  12.028  -4.475  1.00 29.17           C
ATOM     66  NE2 GLN A   9      10.896  11.863  -5.726  1.00 29.46           N
ATOM     67  OE1 GLN A   9      11.048  13.025  -3.800  1.00 31.02           O
TER
ATOM   1719  C1  0XB B 220       6.613   3.931 -16.928  1.00 11.35           C
ATOM   1720  C2  0XB B 220       7.042   5.128 -16.070  1.00 14.60           C
ATOM   1721  O2  0XB B 220       6.347   5.144 -14.862  1.00 15.67           O
ATOM   1722  C3  0XB B 220       6.767   6.445 -16.786  1.00 17.91           C
ATOM   1723  O3  0XB B 220       7.304   7.499 -15.962  1.00 20.75           O
ATOM   1724  C4  0XB B 220       7.275   6.470 -18.142  1.00 17.97           C
ATOM   1725  O4  0XB B 220       6.793   7.605 -18.882  1.00 21.45           O
ATOM   1726  C5  0XB B 220       6.856   5.264 -18.860  1.00 15.05           C
ATOM   1727  O5  0XB B 220       7.286   4.049 -18.182  1.00 12.43           O

Thanks in advance!

[PyMOL] Thermal ellipsoid plot

[koji n. <pas...@gm...>]

Dear all,

The size of isotropic atoms plotted by using "alter all, vdw =
sqrt(b/8)/pi" and "show sphere" looks small compared with the size of
anisotropic atoms displayed by "show ellipsoid" in PyMOL default setting
with 50% probability.

How can I plot the isotropic atoms with 50% probability?

The data is a pdb file converted from a cif through Mercury software.

Thank you very much for your help.

Best regards,
Koji

Re: [PyMOL] pymol in no-gui mode

[James S. <jms...@gm...>]

thank you very much, Ali!
I only changed the quotes in your script because I have integrated it
to my shell script in order to use with the varibables:

  # run pymol to align the snapshots and save it to the session
  pymol -c -d "
  from pymol import cmd
  cmd.load('${sim}/${simulation}_after_minimization.pdb')
  cmd.load('${sim}/${simulation}_after_equilibration.pdb')
  cmd.remove('resn WAT')
  cmd.super('${simulation}_after_equilibration*','${simulation}_after_minimization*')
  cmd.bg_color('white')
  cmd.save('${output}/!!!pymol_sessions/${simulation}_superimposed.pse')
  "

вс, 23 июн. 2019 г. в 12:05, Ali Kusay <aku...@un...>:
>
> Hi James,
>
> Just a follow up, I would still recommend you use the script in a file to do this as it is less messy but it can be done:
>
> pymol -c -d '
> from pymol import cmd
> cmd.load("A.pdb")
> cmd.load("B.pdb")
> cmd.load("C.pdb")
> cmd.super("C*","A*")
> cmd.super("B*","A*")
> cmd.bg_color("white")
> cmd.save("output.pse")
> '
>
> If you paste the above as is in shell It should work provided you are the directory containing the 3 pdb files
>
> Executing pymol with -d flag in shell means you can input pymol commands, to get around indentation you can run leave an ' apostrophe at the end to paste the scripts in and execute all as a string without needing to save as a file
>
> Just for reference, the -c flag is "batch processing (no GUI)" and the commands above can be saved into a python file and ran using:
>
> pymol -c -r  "path_to_script"
>
> Hope this helps.
>
> Cheers,
>
> Ali
> ________________________________________________________________
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
> Email: aku...@un...
>
>
> On 23/6/19, 7:00 pm, "James Starlight" <jms...@gm...> wrote:
>
>     hello there,
>
>     As a part of my scripting routine, I would like to use pymol in no-gui
>     mode (directly in the linux shell) to do the following things:
>     1) load in pymol 3 conformations of the same protein, which are
>     defined as A.pdb B.pdb C.pdb
>     2) superimpose C to A using "super" or alternatively (which is better)
>     "alignall" to A
>     3) change background of the session to white :-)
>     4) save the pymol session for the superimposed A B and C as the *.pse
>     output file
>
>     could you suggest me 1 string command for pymol, which I can directly
>     use in shell terminal to do the mentioned routines in no-gui mode?
>
>     thanks you!!
>
>     James
>
>
>     _______________________________________________
>     PyMOL-users mailing list
>     Archives: http://www.mail-archive.com/pym...@li...
>     Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Re: [PyMOL] pymol in no-gui mode

[Ali K. <aku...@un...>]

Hi James,

Just a follow up, I would still recommend you use the script in a file to do this as it is less messy but it can be done:

pymol -c -d '
from pymol import cmd
cmd.load("A.pdb")
cmd.load("B.pdb")
cmd.load("C.pdb")
cmd.super("C*","A*")
cmd.super("B*","A*")
cmd.bg_color("white")
cmd.save("output.pse")
'

If you paste the above as is in shell It should work provided you are the directory containing the 3 pdb files

Executing pymol with -d flag in shell means you can input pymol commands, to get around indentation you can run leave an ' apostrophe at the end to paste the scripts in and execute all as a string without needing to save as a file

Just for reference, the -c flag is "batch processing (no GUI)" and the commands above can be saved into a python file and ran using:

pymol -c -r  "path_to_script"

Hope this helps.

Cheers,

Ali
________________________________________________________________

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
Email: aku...@un...


On 23/6/19, 7:00 pm, "James Starlight" <jms...@gm...> wrote:

    hello there,
    
    As a part of my scripting routine, I would like to use pymol in no-gui
    mode (directly in the linux shell) to do the following things:
    1) load in pymol 3 conformations of the same protein, which are
    defined as A.pdb B.pdb C.pdb
    2) superimpose C to A using "super" or alternatively (which is better)
    "alignall" to A
    3) change background of the session to white :-)
    4) save the pymol session for the superimposed A B and C as the *.pse
    output file
    
    could you suggest me 1 string command for pymol, which I can directly
    use in shell terminal to do the mentioned routines in no-gui mode?
    
    thanks you!!
    
    James
    
    
    _______________________________________________
    PyMOL-users mailing list
    Archives: http://www.mail-archive.com/pym...@li...
    Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
    

[PyMOL] pymol in no-gui mode

[James S. <jms...@gm...>]

hello there,

As a part of my scripting routine, I would like to use pymol in no-gui
mode (directly in the linux shell) to do the following things:
1) load in pymol 3 conformations of the same protein, which are
defined as A.pdb B.pdb C.pdb
2) superimpose C to A using "super" or alternatively (which is better)
"alignall" to A
3) change background of the session to white :-)
4) save the pymol session for the superimposed A B and C as the *.pse
output file

could you suggest me 1 string command for pymol, which I can directly
use in shell terminal to do the mentioned routines in no-gui mode?

thanks you!!

James

[PyMOL] 2nd Call For Papers - 26th Annual Tcl/Tk Conference (Tcl'2019)

[<con...@tc...>]

Hello pymol-users, fyi ...

26th Annual Tcl/Tk Conference (Tcl'2019)
https://www.tcl-lang.org/community/tcl2019/

November 04 - 08, 2019
Crowne Plaza Houston River Oaks
2712 Southwest Freeway, 77098
Houston, Texas, USA

[ NEWS
 * Our keynote speaker is [Will Duquette](https://github.com/wduquette)
   talking about "Tcl, Rust, and the Death of Rube Goldberg"

 * [Submission is open](https://www.tcl-lang.org/community/tcl2019/cfp.html)
]

Important Dates:

Abstracts and proposals due   September 09, 2019
Notification to authors       September 16, 2019
WIP and BOF reservations open August 12, 2019     ** may change **
Registration opens            September 09, 2019     ** may change **
Author materials due          October 14, 2019
Tutorials Start               November 04, 2019
Conference starts             November 06, 2019

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

Submission of Summaries

Tcl/Tk 2019 will be held in Houston, Texas, USA from November 04, 2019 to November 08, 2019.

The program committee is asking for papers and presentation proposals
from anyone using or developing with Tcl/Tk (and extensions). Past
conferences (Proceedings: https://www.tcl-lang.org/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 September 09, 2019. Authors of accepted
abstracts will have until October 14, 2019 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
	https://www.tcl-lang.org/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 August 12, 2019. Specific instructions for reserving WIP
and BOF time slots will be provided in the registration information
available in August 12, 2019. 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 (https://www.tcl-lang.org/community/tcl2019/) 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: https://code.activestate.com/lists/tcl-announce
for list information, archive, and subscription.

Conference Committee

   * Andreas Kupries
   * Arjen Markus    Deltares
   * Brian Griffin   Mentor - A Siemens Business
   * Gerald Lester   KnG Consulting LLC
   * Joe Mistachkin  Mistachkin Systems
   * Ronald Fox      CAEN Technologies
                     NSCL @ Michigan State University

Contact Information     tcl...@go...

Tcl'2019 would like to thank those who are sponsoring the conference:

   * FlightAware
   * Mentor - A Siemens Business
   * Noumena Corp

[PyMOL] Scripting: printing progress of a slow function

[Lorenzo G. <br...@gm...>]

Dear pymol users,

I'm working on a script that often requires a long time to execute. As I
wait for the underlying issue to be addressed in the upstream repository, I
would like to give the user some sort of a progress bar to let them know
the program did not crash. Unfortunately, pymol seems to freeze completely
every time a function is run, and you can only see the real-time output in
the terminal (only if you actually launched it from a terminal...).

Moreover, the pymol console doesn't seem to accept carriage returns, which
just seem to print new lines as normal.

Did anyone have this problem before? What do you suggest is the best way to
tackle this? Is there a way to un-free pymol while it's crunching numbers?

Thank you,
Lorenzo

Re: [PyMOL] Question about Pymol method / ESP rendering

[Taka S. <ser...@gm...>]

Hi Thomas,
Thank you for your reply.
I made the cube file by using psi4 which is one of quantum chemistry
package.
I will check the file.

Kind regards,
Taka

2019年6月11日(火) 19:40 Thomas Holder <tho...@sc...>:

> Hi Taka,
>
> Your ESP.cube file doesn't look like an electrostatic potential map, it
> looks like electron density. You need two map files, one for the density,
> and one for the ESP.
>
> Cheers,
>   Thomas
>
> > On Jun 8, 2019, at 12:39 AM, Taka Seri <ser...@gm...> wrote:
> >
> > Dear Pymol users,
> > I am newbie of Pymol.
> > I have a question of coloring method. I would like to draw isosurface
> with ESP and would like to set color with ramp_new function.
> > Attached files are example.
> > When I load ESP file and type following command, I could get isosurface.
> > But I could get only blue colored surface after setting color with
> ramp_new function.
> >
> > > isosurface esp_surf, ESP, 0.2
> > > ramp_new color_map, ESP, [-0.1, 0.1]
> >
> > I read following url and it worked well.
> > https://pymolwiki.org/index.php/Ramp_New
> >
> > Is something wrong in my ESP file or approach? Any advice or suggestions
> will be greatly appreciated.
> >
> > Kind regards,
> >
> > Taka
> > <ESP.cube>_______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

[PyMOL] "Qt not available, using GLUT/Tk interface" error

[sunyeping <sun...@al...>]

Dear all,

I installed pymol according to guide at https://pymolwiki.org/index.php/Linux_Install. When I launched pymol, and get the "Qt not available, using GLUT/Tk interface" error and no pymol GUI appeared. How could I deal with this problem?

Best regards

Re: [PyMOL] possible bug mouse coordinates

[Thomas H. <tho...@sc...>]

Hi Arnaud,

This should be fixed now, see
https://github.com/schrodinger/pymol-open-source/commit/af28e453c6

Cheers,
  Thomas

> On Jun 13, 2019, at 5:46 PM, Thomas Holder <tho...@sc...> wrote:
> 
> Hi Arnaud,
> 
> I can reproduce both issues, at least with "sticks" representation. Apparently PyMOL is missing pick color invalidation somewhere.
> 
> As a workaround, click the "Rebuild" button (upper right button box), or type the "rebuild" command. After that, picking should be correct again.
> 
> Cheers,
>  Thomas
> 
>> On Jun 13, 2019, at 4:21 PM, Arnaud Basle <arn...@nc...> wrote:
>> 
>> Dear All,
>> 
>> We found that our home compiled version has the problem just even doing:
>> 
>> load a pdb
>> 
>> change the colour
>> 
>> and then the mouse coordinates are wrong... Anyone else?
>> 
>> Cheers,
>> 
>> Arnaud
>> 
>> 
>> On 13/06/2019 14:33, Arnaud Basle wrote:
>>> Dear All,
>>> 
>>> We may have found a bug where pymol does not get the correct mouse location on the screen.
>>> 
>>> We are using Version 2.3.0a0 on linux Mint 19 (~ubuntu).
>>> 
>>> Maybe people can try to reproduce the bug:
>>> 
>>> open a pdb file
>>> 
>>> display sticks
>>> 
>>> try to select residues or recenter and it should work fine.
>>> 
>>> Now, reduce the top part window of pymol with the log output, movie buttons and command line (the mouse pointer will change then click and drag).
>>> 
>>> repeat selecting/centering and it should work.
>>> 
>>> Then use a menu entry, for example Display>Background>White
>>> 
>>> And if not only us now it seems we click on a residue but another one is selected. It looks like there is a bug where pymol cannot determine the correct mouse co-ordinates?
>>> 
>>> Cheers,
>>> 
>>> Arnaud
>>> 
>>> 
>> -- 
>> Dr Arnaud Basle                     X-ray facilities manager
>> Newcastle Structural Biology Laboratory
>> University of Newcastle
>> Medical School
>> ICAMB
>> Framlington place
>> NE2 4HH Newcastle upon tyne
>> Phone 0191 208 8931
>> 
>> 
>> 
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Advice on plugin creation

[Thomas H. <tho...@sc...>]

Hi Ed,

The tutorial doesn't consider that the "dialog" variable must not go out of scope. It needs an additional reference to keep it alive, e.g. a global will work:

dialog = None

def run_plugin_gui():
   from pymol.Qt import QtWidgets

   global dialog

   if dialog is None:
       dialog = QtWidgets.QDialog()
       # TODO: FILL DIALOG WITH WIDGETS HERE

   dialog.show()

The full example plugin on github doesn't suffer from this problem, it's kept alive by circular references - at least until you run the Python garbage collector (ouch!).

Cheers,
  Thomas


On Wed, Jun 12, 2019 at 7:02 PM Edward Lowe <edw...@bi...> wrote:
> 
> Hello,
> 
> I'm trying to create what I think should be a fairly simple plugin to
> use pymol to showcase structures for a University Open day - all it
> needs to do is load up coordinate files and maps and present a very
> simple GUI that visitors can use to move between pre-defined scenes.
> 
> I've constructed a PyQt plugin following the tutorial on pymolwiki
> which works up to a point...
> If I display the window using dialog.show() as in the tutorial example,
> the window disappears immediately on opening.
> If I change this to using dialog.exec() my widget opens correctly and
> everything works - but since this is now a modal window it is not
> possible to return to the main pymol gui and interact with the
> structure.  This was the point of the exercise an why I'm not just
> making a movie!
> 
> Does anyone have any advice on what could be done to fix this
> behaviour?  It probably goes without saying that I am very much a
> novice at this!
> 
> Thanks,
> Ed.
> --
> Dr. E.D. Lowe                   edw...@bi...
> Department of Biochemistry      Tel: ++44 (0)1865 (2)75392
> University of Oxford
> Oxford UK, OX1 3QU
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe


--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] possible bug mouse coordinates

[Thomas H. <tho...@sc...>]

Hi Arnaud,

I can reproduce both issues, at least with "sticks" representation. Apparently PyMOL is missing pick color invalidation somewhere.

As a workaround, click the "Rebuild" button (upper right button box), or type the "rebuild" command. After that, picking should be correct again.

Cheers,
  Thomas

> On Jun 13, 2019, at 4:21 PM, Arnaud Basle <arn...@nc...> wrote:
> 
> Dear All,
> 
> We found that our home compiled version has the problem just even doing:
> 
> load a pdb
> 
> change the colour
> 
> and then the mouse coordinates are wrong... Anyone else?
> 
> Cheers,
> 
> Arnaud
> 
> 
> On 13/06/2019 14:33, Arnaud Basle wrote:
>> Dear All,
>> 
>> We may have found a bug where pymol does not get the correct mouse location on the screen.
>> 
>> We are using Version 2.3.0a0 on linux Mint 19 (~ubuntu).
>> 
>> Maybe people can try to reproduce the bug:
>> 
>> open a pdb file
>> 
>> display sticks
>> 
>> try to select residues or recenter and it should work fine.
>> 
>> Now, reduce the top part window of pymol with the log output, movie buttons and command line (the mouse pointer will change then click and drag).
>> 
>> repeat selecting/centering and it should work.
>> 
>> Then use a menu entry, for example Display>Background>White
>> 
>> And if not only us now it seems we click on a residue but another one is selected. It looks like there is a bug where pymol cannot determine the correct mouse co-ordinates?
>> 
>> Cheers,
>> 
>> Arnaud
>> 
>> 
> -- 
> Dr Arnaud Basle                     X-ray facilities manager
> Newcastle Structural Biology Laboratory
> University of Newcastle
> Medical School
> ICAMB
> Framlington place
> NE2 4HH Newcastle upon tyne
> Phone 0191 208 8931
> 
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] possible bug mouse coordinates

[Arnaud B. <arn...@nc...>]

Dear All,

We found that our home compiled version has the problem just even doing:

load a pdb

change the colour

and then the mouse coordinates are wrong... Anyone else?

Cheers,

Arnaud


On 13/06/2019 14:33, Arnaud Basle wrote:
> Dear All,
>
> We may have found a bug where pymol does not get the correct mouse 
> location on the screen.
>
> We are using Version 2.3.0a0 on linux Mint 19 (~ubuntu).
>
> Maybe people can try to reproduce the bug:
>
> open a pdb file
>
> display sticks
>
> try to select residues or recenter and it should work fine.
>
> Now, reduce the top part window of pymol with the log output, movie 
> buttons and command line (the mouse pointer will change then click and 
> drag).
>
> repeat selecting/centering and it should work.
>
> Then use a menu entry, for example Display>Background>White
>
> And if not only us now it seems we click on a residue but another one 
> is selected. It looks like there is a bug where pymol cannot determine 
> the correct mouse co-ordinates?
>
> Cheers,
>
> Arnaud
>
>
-- 
Dr Arnaud Basle                     X-ray facilities manager
Newcastle Structural Biology Laboratory
University of Newcastle
Medical School
ICAMB
Framlington place
NE2 4HH Newcastle upon tyne
Phone 0191 208 8931

[PyMOL] possible bug mouse coordinates

[Arnaud B. <arn...@nc...>]

Dear All,

We may have found a bug where pymol does not get the correct mouse 
location on the screen.

We are using Version 2.3.0a0 on linux Mint 19 (~ubuntu).

Maybe people can try to reproduce the bug:

open a pdb file

display sticks

try to select residues or recenter and it should work fine.

Now, reduce the top part window of pymol with the log output, movie 
buttons and command line (the mouse pointer will change then click and 
drag).

repeat selecting/centering and it should work.

Then use a menu entry, for example Display>Background>White

And if not only us now it seems we click on a residue but another one is 
selected. It looks like there is a bug where pymol cannot determine the 
correct mouse co-ordinates?

Cheers,

Arnaud


-- 
Dr Arnaud Basle                     X-ray facilities manager
Newcastle Structural Biology Laboratory
University of Newcastle
Medical School
ICAMB
Framlington place
NE2 4HH Newcastle upon tyne
Phone 0191 208 8931

[PyMOL] Advice on plugin creation

[Edward L. <edw...@bi...>]

Hello,

I'm trying to create what I think should be a fairly simple plugin to
use pymol to showcase structures for a University Open day - all it
needs to do is load up coordinate files and maps and present a very
simple GUI that visitors can use to move between pre-defined scenes.

I've constructed a PyQt plugin following the tutorial on pymolwiki
which works up to a point... 
If I display the window using dialog.show() as in the tutorial example,
the window disappears immediately on opening.
If I change this to using dialog.exec() my widget opens correctly and
everything works - but since this is now a modal window it is not
possible to return to the main pymol gui and interact with the
structure.  This was the point of the exercise an why I'm not just
making a movie!

Does anyone have any advice on what could be done to fix this
behaviour?  It probably goes without saying that I am very much a
novice at this!

Thanks,
Ed.
-- 
Dr. E.D. Lowe			edw...@bi...
Department of Biochemistry	Tel: ++44 (0)1865 (2)75392
University of Oxford
Oxford UK, OX1 3QU

Re: [PyMOL] Question about Pymol method / ESP rendering

[Thomas H. <tho...@sc...>]

Hi Taka,

Your ESP.cube file doesn't look like an electrostatic potential map, it looks like electron density. You need two map files, one for the density, and one for the ESP.

Cheers,
  Thomas

> On Jun 8, 2019, at 12:39 AM, Taka Seri <ser...@gm...> wrote:
> 
> Dear Pymol users,
> I am newbie of Pymol.
> I have a question of coloring method. I would like to draw isosurface with ESP and would like to set color with ramp_new function.
> Attached files are example.
> When I load ESP file and type following command, I could get isosurface.
> But I could get only blue colored surface after setting color with ramp_new function.
> 
> > isosurface esp_surf, ESP, 0.2
> > ramp_new color_map, ESP, [-0.1, 0.1]
> 
> I read following url and it worked well.
> https://pymolwiki.org/index.php/Ramp_New
> 
> Is something wrong in my ESP file or approach? Any advice or suggestions will be greatly appreciated.
> 
> Kind regards,
> 
> Taka
> <ESP.cube>_______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] Question about Pymol method / ESP rendering

[Taka S. <ser...@gm...>]

Dear Pymol users,
I am newbie of Pymol.
I have a question of coloring method. I would like to draw isosurface with
ESP and would like to set color with ramp_new function.
Attached files are example.
When I load ESP file and type following command, I could get isosurface.
But I could get only blue colored surface after setting color with ramp_new
function.

> isosurface esp_surf, ESP, 0.2
> ramp_new color_map, ESP, [-0.1, 0.1]

I read following url and it worked well.
https://pymolwiki.org/index.php/Ramp_New

Is something wrong in my ESP file or approach? Any advice or suggestions
will be greatly appreciated.

Kind regards,

Taka

Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol?

[h. a. s. <h.a...@gm...>]

When you use the alter command, then rebuild, and then save the PyMOL session as a .pse file, the changes will be written into the .pse file. They will not be lost when you reopen the .pse file.

The alter command doesn’t do anything to the actual .pdb or .cif file. It’s my understanding that when you open a structure file in PyMOL, it reads the pdb or cif file and then assigns appropriate secondary structure based on the phi and psi angles of the protein backbone.

> On Jun 5, 2019, at 11:50 PM, sunyeping <sun...@al...> wrote:
> 
> Thank you for the reply.
> 
> Do alter and rebuild commands really change the secondary structure of the specific residues or they just change the display? I saved the structure altered bt the alter and rebuild commands, but when I open the structure agian in pymol, the residues I changes are still displayed as in the original structure file.
> 
> Best regards 
> ------------------------------------------------------------------
> From:h. adam steinberg <h.a...@gm...>
> Sent At:2019 Jun. 5 (Wed.) 20:43
> To:孙业平 <sun...@al...>; pymol-users <pym...@li...>
> Subject:Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol?
> 
> It’s the same command but just change the “S” to an “H”. Or you can use a “L” if you want a loop (unstructured).
> 
> alter 3-10/, ss=‘H’ 
> 
> You also need to enter the command: rebuild, to redraw the structure on your screen. Use rebuild after you enter the alter command.
> 
> 
> On Jun 4, 2019, at 10:37 PM, sunyeping via PyMOL-users <pym...@li... <mailto:pym...@li...>> wrote:
> 
> Dear pymol user,
> 
> I wonder why sometimes the secondary structure of a protein can not be displayed incorrect in pymol. I have a structure, some residues are predicted to be sheet or 3-10 helix with DSSP, but they are displayed as loop. Only typing "dss" command in pymol doesn't work. I know by using the "alter" commad the secondary structures can be assigned. The following command:
> 
> alter 61-63/, ss='S' 
> 
> can assign residue 61-63 as sheet. However, what is the command to assign residues as 3-10 helix?
> 
> Thank you in advance.
> 
> Arthur
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...>
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>
> 

Re: [PyMOL] colored secondary structure of two chains with different colors [resolved]

[ABEL S. <Ste...@ce...>]

Thank you vevry much Annemarie  it worked 

----------------------------------------------------------
Stéphane Abel, Ph.D.
Commissariat à l’Energie Atomique et aux Energies Alternatives
Centre de Saclay DSV/ISVFJ/SB2SM
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60

----------------------------------------------------------------------

Message: 1
Date: Thu, 6 Jun 2019 12:49:56 +0200
From: ahoneg <ann...@uz...>
To: pym...@li...
Subject: [PyMOL] colored secondary structure of two chains with
        different colors
Message-ID: <C34...@uz...>
Content-Type: text/plain;       charset=utf-8

Dear St?phane,

by default, the cartoon representation takes its color from the color of the c-alpha atoms of your protein.
However, you can override this default and assign a specific color to the cartoon representation of a given selection by:

set cartoon_color, color, (selection)

e.g.

set cartoon_color, red, resi 1-60

best regards

Annemarie Honegger
____________________________________________________________

Dr. Annemarie Honegger
Dept. of Biochemistry
Z?rich University
Winterthurerstrasse 190
8057 Z?rich
Switzerland

e-mail:   hon...@bi...
phone:   +41 44 635 55 62
fax:        +41 44 635 57 12


>
> Message: 4
> Date: Thu, 6 Jun 2019 10:26:29 +0000
> From: ABEL Stephane <Ste...@ce...>
> To: "h. adam steinberg" <h.a...@gm...>
> Cc: "pym...@li..."
>       <pym...@li...>
> Subject: Re: [PyMOL] colored secondary structure of two chains with
>       different colors
> Message-ID:
>       <3E3...@EX...>
> Content-Type: text/plain; charset="Windows-1252"
>
> Hi Adam
>
> OK I can colored each chain with different colors. But it is not exactly what I want. Indeed in the figure*
>
> - the AA are  in sticks with the different colors for each atom --> I can do this
> - the beta sheet in the monomer are in red and blue ---> I can "not" do this even if I use your suggestion
>
> I would like in two representations at the same time and the necessary commands for adding them in a script.
> ript.
>
> *https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>
> Thank you again.
>
> St?phane
>
>
> ----------------------------------------------------------
> St?phane Abel, Ph.D.
> Commissariat ? l?Energie Atomique et aux Energies Alternatives
> Centre de Saclay DSV/ISVFJ/SB2SM
> Bat 528, Office 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
> ________________________________________
> De : h. adam steinberg [h.a...@gm...]
> Envoy? : mercredi 5 juin 2019 21:36
> ? : ABEL Stephane
> Objet : Re: [PyMOL] colored secondary structure of two chains with different colors
>
> If you change your mouse / selection mode to chains, you can then click on one of the monomers and choose a color for it from the (sale) in the right side panel drop down menu. Then click on the other monomer and do the same.
>
> Is that what you are asking for?
>
>> On Jun 5, 2019, at 1:23 PM, ABEL Stephane <Ste...@ce...> wrote:
>>
>> Hello all
>>
>> I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to color the  beta sheets of each monomer with different colors (for instance in red and blue colors) in Figure
>>
>> https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>>
>> How to do this ?
>>
>> Thank you
>>
>> St?phane
>>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
>
> ------------------------------
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> ------------------------------
>
> End of PyMOL-users Digest, Vol 157, Issue 5
> *******************************************




------------------------------



------------------------------

Subject: Digest Footer

_______________________________________________
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------------------------------

End of PyMOL-users Digest, Vol 157, Issue 6
*******************************************

Re: [PyMOL] PyMOL-users Digest, Vol 157, Issue 6

[ABEL S. <Ste...@ce...>]

Dear Annemarie, 

Thank you very much it worked !!! 

Stéphane

----------------------------------------------------------
Stéphane Abel, Ph.D.
Commissariat à l’Energie Atomique et aux Energies Alternatives
Centre de Saclay DSV/ISVFJ/SB2SM
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60


----------------------------------------------------------------------

Message: 1
Date: Thu, 6 Jun 2019 12:49:56 +0200
From: ahoneg <ann...@uz...>
To: pym...@li...
Subject: [PyMOL] colored secondary structure of two chains with
        different colors
Message-ID: <C34...@uz...>
Content-Type: text/plain;       charset=utf-8

Dear St?phane,

by default, the cartoon representation takes its color from the color of the c-alpha atoms of your protein.
However, you can override this default and assign a specific color to the cartoon representation of a given selection by:

set cartoon_color, color, (selection)

e.g.

set cartoon_color, red, resi 1-60

best regards

Annemarie Honegger
____________________________________________________________

Dr. Annemarie Honegger
Dept. of Biochemistry
Z?rich University
Winterthurerstrasse 190
8057 Z?rich
Switzerland

e-mail:   hon...@bi...
phone:   +41 44 635 55 62
fax:        +41 44 635 57 12


>
> Message: 4
> Date: Thu, 6 Jun 2019 10:26:29 +0000
> From: ABEL Stephane <Ste...@ce...>
> To: "h. adam steinberg" <h.a...@gm...>
> Cc: "pym...@li..."
>       <pym...@li...>
> Subject: Re: [PyMOL] colored secondary structure of two chains with
>       different colors
> Message-ID:
>       <3E3...@EX...>
> Content-Type: text/plain; charset="Windows-1252"
>
> Hi Adam
>
> OK I can colored each chain with different colors. But it is not exactly what I want. Indeed in the figure*
>
> - the AA are  in sticks with the different colors for each atom --> I can do this
> - the beta sheet in the monomer are in red and blue ---> I can "not" do this even if I use your suggestion
>
> I would like in two representations at the same time and the necessary commands for adding them in a script.
> ript.
>
> *https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>
> Thank you again.
>
> St?phane
>
>
> ----------------------------------------------------------
> St?phane Abel, Ph.D.
> Commissariat ? l?Energie Atomique et aux Energies Alternatives
> Centre de Saclay DSV/ISVFJ/SB2SM
> Bat 528, Office 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
> ________________________________________
> De : h. adam steinberg [h.a...@gm...]
> Envoy? : mercredi 5 juin 2019 21:36
> ? : ABEL Stephane
> Objet : Re: [PyMOL] colored secondary structure of two chains with different colors
>
> If you change your mouse / selection mode to chains, you can then click on one of the monomers and choose a color for it from the (sale) in the right side panel drop down menu. Then click on the other monomer and do the same.
>
> Is that what you are asking for?
>
>> On Jun 5, 2019, at 1:23 PM, ABEL Stephane <Ste...@ce...> wrote:
>>
>> Hello all
>>
>> I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to color the  beta sheets of each monomer with different colors (for instance in red and blue colors) in Figure
>>
>> https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>>
>> How to do this ?
>>
>> Thank you
>>
>> St?phane
>>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
>
> ------------------------------
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> ------------------------------
>
> End of PyMOL-users Digest, Vol 157, Issue 5
> *******************************************




------------------------------



------------------------------

Subject: Digest Footer

_______________________________________________
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Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

------------------------------

End of PyMOL-users Digest, Vol 157, Issue 6
*******************************************

[PyMOL] colored secondary structure of two chains with different colors

[ahoneg <ann...@uz...>]

Dear Stéphane,

by default, the cartoon representation takes its color from the color of the c-alpha atoms of your protein. 
However, you can override this default and assign a specific color to the cartoon representation of a given selection by:

set cartoon_color, color, (selection)

e.g.

set cartoon_color, red, resi 1-60

best regards

Annemarie Honegger
____________________________________________________________

Dr. Annemarie Honegger
Dept. of Biochemistry
Zürich University
Winterthurerstrasse 190
8057 Zürich
Switzerland

e-mail:   hon...@bi...
phone:   +41 44 635 55 62
fax:        +41 44 635 57 12     


> 
> Message: 4
> Date: Thu, 6 Jun 2019 10:26:29 +0000
> From: ABEL Stephane <Ste...@ce...>
> To: "h. adam steinberg" <h.a...@gm...>
> Cc: "pym...@li..."
> 	<pym...@li...>
> Subject: Re: [PyMOL] colored secondary structure of two chains with
> 	different colors
> Message-ID:
> 	<3E3...@EX...>
> Content-Type: text/plain; charset="Windows-1252"
> 
> Hi Adam 
> 
> OK I can colored each chain with different colors. But it is not exactly what I want. Indeed in the figure* 
> 
> - the AA are  in sticks with the different colors for each atom --> I can do this 
> - the beta sheet in the monomer are in red and blue ---> I can "not" do this even if I use your suggestion
> 
> I would like in two representations at the same time and the necessary commands for adding them in a script. 
> ript. 
> 
> *https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
> 
> Thank you again. 
> 
> St?phane
> 
> 
> ----------------------------------------------------------
> St?phane Abel, Ph.D.
> Commissariat ? l?Energie Atomique et aux Energies Alternatives
> Centre de Saclay DSV/ISVFJ/SB2SM
> Bat 528, Office 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
> ________________________________________
> De : h. adam steinberg [h.a...@gm...]
> Envoy? : mercredi 5 juin 2019 21:36
> ? : ABEL Stephane
> Objet : Re: [PyMOL] colored secondary structure of two chains with different colors
> 
> If you change your mouse / selection mode to chains, you can then click on one of the monomers and choose a color for it from the (sale) in the right side panel drop down menu. Then click on the other monomer and do the same.
> 
> Is that what you are asking for?
> 
>> On Jun 5, 2019, at 1:23 PM, ABEL Stephane <Ste...@ce...> wrote:
>> 
>> Hello all
>> 
>> I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to color the  beta sheets of each monomer with different colors (for instance in red and blue colors) in Figure
>> 
>> https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>> 
>> How to do this ?
>> 
>> Thank you
>> 
>> St?phane
>> 
>> 
>> 
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 
> 
> 
> 
> ------------------------------
> 
> 
> 
> ------------------------------
> 
> Subject: Digest Footer
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 
> ------------------------------
> 
> End of PyMOL-users Digest, Vol 157, Issue 5
> *******************************************

Re: [PyMOL] colored secondary structure of two chains with different colors

[ABEL S. <Ste...@ce...>]

Hi Adam 

OK I can colored each chain with different colors. But it is not exactly what I want. Indeed in the figure* 

- the AA are  in sticks with the different colors for each atom --> I can do this 
- the beta sheet in the monomer are in red and blue ---> I can "not" do this even if I use your suggestion

I would like in two representations at the same time and the necessary commands for adding them in a script. 
ript. 

*https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg

Thank you again. 

Stéphane


----------------------------------------------------------
Stéphane Abel, Ph.D.
Commissariat à l’Energie Atomique et aux Energies Alternatives
Centre de Saclay DSV/ISVFJ/SB2SM
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
________________________________________
De : h. adam steinberg [h.a...@gm...]
Envoyé : mercredi 5 juin 2019 21:36
À : ABEL Stephane
Objet : Re: [PyMOL] colored secondary structure of two chains with different colors

If you change your mouse / selection mode to chains, you can then click on one of the monomers and choose a color for it from the (sale) in the right side panel drop down menu. Then click on the other monomer and do the same.

Is that what you are asking for?

> On Jun 5, 2019, at 1:23 PM, ABEL Stephane <Ste...@ce...> wrote:
>
> Hello all
>
> I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to color the  beta sheets of each monomer with different colors (for instance in red and blue colors) in Figure
>
> https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>
> How to do this ?
>
> Thank you
>
> Stéphane
>
>
>
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> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
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Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol?

[sunyeping <sun...@al...>]

Thank you for the reply. 

Do alter and rebuild commands really change the secondary structure of the specific residues or they just change the display? I saved the structure altered bt the alter and rebuild commands, but when I open the structure agian in pymol, the residues I changes are still displayed as in the original structure file.

Best regards 
------------------------------------------------------------------
From:h. adam steinberg <h.a...@gm...>
Sent At:2019 Jun. 5 (Wed.) 20:43
To:孙业平 <sun...@al...>; pymol-users <pym...@li...>
Subject:Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol?

It’s the same command but just change the “S” to an “H”. Or you can use a “L” if you want a loop (unstructured).

alter 3-10/, ss=‘H’ 

You also need to enter the command: rebuild, to redraw the structure on your screen. Use rebuild after you enter the alter command.


On Jun 4, 2019, at 10:37 PM, sunyeping via PyMOL-users <pym...@li...> wrote:
Dear pymol user,

I wonder why sometimes the secondary structure of a protein can not be displayed incorrect in pymol. I have a structure, some residues are predicted to be sheet or 3-10 helix with DSSP, but they are displayed as loop. Only typing "dss" command in pymol doesn't work. I know by using the "alter" commad the secondary structures can be assigned. The following command:

alter 61-63/, ss='S' 

can assign residue 61-63 as sheet. However, what is the command to assign residues as 3-10 helix?

Thank you in advance.

Arthur_______________________________________________
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[PyMOL] colored secondary structure of two chains with different colors

[ABEL S. <Ste...@ce...>]

Hello all

I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to color the  beta sheets of each monomer with different colors (for instance in red and blue colors) in Figure 

https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg

How to do this ?

Thank you 

Stéphane

Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol?

[h. a. s. <h.a...@gm...>]

It’s the same command but just change the “S” to an “H”. Or you can use a “L” if you want a loop (unstructured).

alter 3-10/, ss=‘H’ 

You also need to enter the command: rebuild, to redraw the structure on your screen. Use rebuild after you enter the alter command.


> On Jun 4, 2019, at 10:37 PM, sunyeping via PyMOL-users <pym...@li...> wrote:
> 
> Dear pymol user,
> 
> I wonder why sometimes the secondary structure of a protein can not be displayed incorrect in pymol. I have a structure, some residues are predicted to be sheet or 3-10 helix with DSSP, but they are displayed as loop. Only typing "dss" command in pymol doesn't work. I know by using the "alter" commad the secondary structures can be assigned. The following command:
> 
> alter 61-63/, ss='S' 
> 
> can assign residue 61-63 as sheet. However, what is the command to assign residues as 3-10 helix?
> 
> Thank you in advance.
> 
> Arthur
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe