pymol-users Mailing List for PyMOL Molecular Graphics System

Thanks Jared. A lot of fantastic tips there. Much appreciated.

Regards.

On Sat, Apr 29, 2017 at 6:03 AM, Jared Sampson
<jar...@co...> wrote:
> Hi Ahmad -
>
> Here are a few suggestions:
>
> I'm still a bit new to the API so I'm not sure which commands to use.
> At least I know I will start with cmd.select(string name, string
> selection).
>
> How can I tell Pymol to:
>
> 1) look within a certain radius distance, and return resi's within
> that distacne.
>
>
>     cmd.select('mysele', 'byres all within 5 of sele')
>
> See https://pymolwiki.org/index.php/Selection_Algebra for more handy
> operators (`beyond`, `around`, `expand`, etc.)
>
>
> 2) find all polar interactions within a distance,
>
>
> You can use cmd.distance (https://pymolwiki.org/index.php/Distance), e.g.
> (as done in the GUI by [A] > find > polar contacts...)
>
>     cmd.dist("mysele_polar_conts","mysele","all within 5 of
> mysele",quiet=1,mode=2,label=0,reset=1)
>
> or for a list of atoms, check out https://pymolwiki.org/index.php/Polarpairs
>
>
> use sticks,
>
>
>     cmd.show('sticks', 'mysele')
>
> or to hide all other representations,
>
>     cmd.show_as('sticks', 'mysele')
>
>
> color by atom
>
>
>     util.cnc('mysele')
>
> I use this one all the time ("cnc" == color non-carbon).  There is also
> `util.cbc` == color by chain.
>
>
> hide everything else
>
>
>     cmd.hide('everything', 'all and not mysele')
>
>
> and output an image of the selections and interactions around it.
>
>
>     cmd.zoom('mysele', 5)
>     cmd.png('mysele.png', ray=1)
>
>
> Please feel free to throw in any useful commands that can you might think is
> helpful.
>
>
> One useful trick to learn new commands is to open a log file (via `log_open
> log.pml` or the File menu) and then perform the desired action in the GUI.
> The log file will show the API commands that are called from the GUI.  It
> doesn't work for everything (e.g. wizards), but for most basic actions, it
> should be helpful.  At least it will give you the right command to look up
> on the PyMOL wiki!
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> Your help is greatly appreciated.
>
> 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 Ahmad - 

Here are a few suggestions:

> I'm still a bit new to the API so I'm not sure which commands to use.
> At least I know I will start with cmd.select(string name, string
> selection).
> 
> How can I tell Pymol to:
> 
> 1) look within a certain radius distance, and return resi's within
> that distacne.

    cmd.select('mysele', 'byres all within 5 of sele')

See https://pymolwiki.org/index.php/Selection_Algebra <" rel="nofollow">https://pymolwiki.org/index.php/Selection_Algebra> for more handy operators (`beyond`, `around`, `expand`, etc.)


> 2) find all polar interactions within a distance,

You can use cmd.distance (https://pymolwiki.org/index.php/Distance <)," rel="nofollow">https://pymolwiki.org/index.php/Distance>), e.g. (as done in the GUI by [A] > find > polar contacts...)

    cmd.dist("mysele_polar_conts","mysele","all within 5 of mysele",quiet=1,mode=2,label=0,reset=1)

or for a list of atoms, check out https://pymolwiki.org/index.php/Polarpairs <" rel="nofollow">https://pymolwiki.org/index.php/Polarpairs>


> use sticks,

    cmd.show('sticks', 'mysele')

or to hide all other representations,

    cmd.show_as('sticks', 'mysele')


> color by atom

    util.cnc('mysele')

I use this one all the time ("cnc" == color non-carbon).  There is also `util.cbc` == color by chain.


> hide everything else

    cmd.hide('everything', 'all and not mysele')


> and output an image of the selections and interactions around it.

    cmd.zoom('mysele', 5)
    cmd.png('mysele.png', ray=1)


> Please feel free to throw in any useful commands that can you might think is helpful.

One useful trick to learn new commands is to open a log file (via `log_open log.pml` or the File menu) and then perform the desired action in the GUI.  The log file will show the API commands that are called from the GUI.  It doesn't work for everything (e.g. wizards), but for most basic actions, it should be helpful.  At least it will give you the right command to look up on the PyMOL wiki!

Hope that helps.

Cheers,
Jared

> 
> Your help is greatly appreciated.
> 
> 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 all,

Thanks to Dheeraj, Jordan and Jed for your advice!

I don't think I installed any "extra" options, just educational-use-only 
PyMOL (version 1.7.4.5, x64) on Windows 10.

In the Windows 10 Start Menu folder, all of the 3D options are in a 
subfolder called "Stereo 3D Launch," so I think it's safe to say that 
all of those shortcuts are "special" and not "typical."

That leaves just 4 options, and of those, "Full Screen" and "Viewer 
Only" seem pretty straightforward.

That only leaves "PyMOL + Tcl-Tk GUI" and "PyMOL + Tcl-Tk GUI + 
Console." It looks like the shortcuts point to the same program, but the 
Console shortcut has an extra switch at the end: "C:\Program 
Files\PyMOL\PyMOL\PymolWin.exe" +2 -J. The GUI-only shortcut doesn't 
have the +2 switch, just the -J switch.

I don't know what the +2 switch does, or what the -J switch does for 
that matter, but I think I'm just going to use the "PyMOL + Tcl-Tk GUI + 
Console" option in the Start Menu for my everyday PyMOL use.

When I open either of these two shortcuts, they look exactly the same to 
me anyway.

Thanks for everyone's help!

AJ



------ Original Message ------
From: "Dheeraj Prakaash" <dh...@gm...>
To: "AJ Vincelli" <AJV...@gm...>
Cc: pym...@li...
Sent: 4/22/2017 12:46:51 AM
Subject: Re: [PyMOL] which PyMOL to open?

>Wow!
>I haven't seen so many options before, even after installing Edu PyMOL 
>correctly.
>
>Do you all of you get these options (Win10 users)?
>I only get to see
>PyMOL + Tcl-tk, and,
>PyMOL + Tcl-tk + Console.
>
>AJ, did you install anything extra?
>This may seem another dumb question, but your answers will be helpful.
>
>Regards
>Dheeraj

Hello,

I'm still a bit new to the API so I'm not sure which commands to use.
At least I know I will start with cmd.select(string name, string
selection).

How can I tell Pymol to:

1) look within a certain radius distance, and return resi's within
that distacne.

2) find all polar interactions within a distance, use sticks, color by
atom, hide everything else and output an image of the selections and
interactions around it.

Please feel free to throw in any useful commands that can you might
think is helpful.

Your help is greatly appreciated.

Regards.

Hi Daniel,

Apparently, no b-factors were assigned, or the CA positions in all states are identical.

Here is a similar script, maybe that works better for you (uses “rmsf2b” from PSICO):

run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/editing.py
fetch 1nmr, async=0
rmsf2b 1nmr
spheroid 1nmr
as cartoon
cartoon putty
spectrum b, blue_white_red, 1nmr & guide

Hope that helps.

Cheers,
  Thomas

> On Apr 27, 2017, at 4:11 PM, Daniel Munoz Escudero <dm...@un...> wrote:
> 
> Hello,
> 
> I found in this repository http://muralab.org/~cmura/PyMOL/ an script (average3d.py) to perform the sausage representation in PyMOL. Although it works perfectly good with the pdbs given in the examples, I couldn't get the same results for my molecule. After performing all the RMSD calculations (I have 51 states in my molecule), the message: " Extrude-Warning: invalid putty settings (division by zero)", appears right after the command: cmd.spectrum('b','blue_white_red','yesfit_ALL and name CA')
> 
> I really don't know what the problem is. Has anyone had a similar problem and could help me out?
> 
> Thank you very much,
> 
> Daniel.

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hello,

I found in this repository http://muralab.org/~cmura/PyMOL/ an script
(average3d.py) to perform the sausage representation in PyMOL. Although it
works perfectly good with the pdbs given in the examples, I couldn't get
the same results for my molecule. After performing all the RMSD
calculations (I have 51 states in my molecule), the message: "
Extrude-Warning: invalid putty settings (division by zero)", appears right
after the command: cmd.spectrum('b','blue_white_red','yesfit_ALL and name
CA')

I really don't know what the problem is. Has anyone had a similar problem
and could help me out?

Thank you very much,

Daniel.

Hi
I am not sure which method is being used by PyMOL but because the
algorithm uses a dot density term it is likely the Shrake & Rupley
algorithm also known as the rolling ball method. You should read the
FreeSASA article (freely available
https://f1000research.com/articles/5-189/v1 ). The author provides a
really nice description of SASA calculations along with precision and
speed analysis.

Emilio

On Thu, Apr 27, 2017 at 7:38 AM, Ahmad Abdelzaher
<und...@gm...> wrote:
> Thank you for your reply. With regard to the algorithm used, do you
> have any idea which algorithm is used in the Pymol calculations? DSSP
> is likely to be using the rolling ball method.
>
> Regards.
>
> On Thu, Apr 27, 2017 at 1:35 PM, Emilio Xavier Esposito
> <emi...@gm...> wrote:
>> Hi
>> The accuracy of the calculation depends on the dot_density value (the
>> amount of sampling done) with 1 being the lowest quality and 4 being
>> the best quality. A dot_density value of 1 uses less computational
>> resources (time) than a dot_density of 4 because of the amount of
>> sampling performed to calculate the surface area.
>>
>> With respect to your question regarding the difference between PyMOL's
>> get_area command and the SASA calculated bye DSSP, these differences
>> in surface area could be the result of different atom radii being
>> used, the inclusion of hydrogen atoms, or differences in the algorithm
>> used to calculate the SASA. The speed differences could be the result
>> of different algorithms and how they are implemented.
>>
>> You might want to check out FreeSASA ( http://freesasa.github.io ) to
>> perform your SASA calculations.
>>
>> Emilio
>>
>> On Wed, Apr 26, 2017 at 11:49 PM, Ahmad Abdelzaher
>> <und...@gm...> wrote:
>>> I would appreciate any help regarding this.
>>>
>>> On Tue, Apr 25, 2017 at 12:36 PM, Ahmad Abdelzaher
>>> <und...@gm...> wrote:
>>>> Hello,
>>>>
>>>> Does the get_area command use the rolling ball algorithm? Which
>>>> dot_density corresponds to the best accuracy 1 or 4? Is there a reason
>>>> why it consumes more time to compute sasa? Dssp takes significantly
>>>> less time to do the calculations, however compared to Pymol
>>>> dot_density of 3, the areas sometimes differ by 4,5,6,  squared
>>>> angstroms!
>>>>
>>>> Any comment on that?
>>>>
>>>> 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...

Thank you for your reply. With regard to the algorithm used, do you
have any idea which algorithm is used in the Pymol calculations? DSSP
is likely to be using the rolling ball method.

Regards.

On Thu, Apr 27, 2017 at 1:35 PM, Emilio Xavier Esposito
<emi...@gm...> wrote:
> Hi
> The accuracy of the calculation depends on the dot_density value (the
> amount of sampling done) with 1 being the lowest quality and 4 being
> the best quality. A dot_density value of 1 uses less computational
> resources (time) than a dot_density of 4 because of the amount of
> sampling performed to calculate the surface area.
>
> With respect to your question regarding the difference between PyMOL's
> get_area command and the SASA calculated bye DSSP, these differences
> in surface area could be the result of different atom radii being
> used, the inclusion of hydrogen atoms, or differences in the algorithm
> used to calculate the SASA. The speed differences could be the result
> of different algorithms and how they are implemented.
>
> You might want to check out FreeSASA ( http://freesasa.github.io ) to
> perform your SASA calculations.
>
> Emilio
>
> On Wed, Apr 26, 2017 at 11:49 PM, Ahmad Abdelzaher
> <und...@gm...> wrote:
>> I would appreciate any help regarding this.
>>
>> On Tue, Apr 25, 2017 at 12:36 PM, Ahmad Abdelzaher
>> <und...@gm...> wrote:
>>> Hello,
>>>
>>> Does the get_area command use the rolling ball algorithm? Which
>>> dot_density corresponds to the best accuracy 1 or 4? Is there a reason
>>> why it consumes more time to compute sasa? Dssp takes significantly
>>> less time to do the calculations, however compared to Pymol
>>> dot_density of 3, the areas sometimes differ by 4,5,6,  squared
>>> angstroms!
>>>
>>> Any comment on that?
>>>
>>> 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
The accuracy of the calculation depends on the dot_density value (the
amount of sampling done) with 1 being the lowest quality and 4 being
the best quality. A dot_density value of 1 uses less computational
resources (time) than a dot_density of 4 because of the amount of
sampling performed to calculate the surface area.

With respect to your question regarding the difference between PyMOL's
get_area command and the SASA calculated bye DSSP, these differences
in surface area could be the result of different atom radii being
used, the inclusion of hydrogen atoms, or differences in the algorithm
used to calculate the SASA. The speed differences could be the result
of different algorithms and how they are implemented.

You might want to check out FreeSASA ( http://freesasa.github.io ) to
perform your SASA calculations.

Emilio

On Wed, Apr 26, 2017 at 11:49 PM, Ahmad Abdelzaher
<und...@gm...> wrote:
> I would appreciate any help regarding this.
>
> On Tue, Apr 25, 2017 at 12:36 PM, Ahmad Abdelzaher
> <und...@gm...> wrote:
>> Hello,
>>
>> Does the get_area command use the rolling ball algorithm? Which
>> dot_density corresponds to the best accuracy 1 or 4? Is there a reason
>> why it consumes more time to compute sasa? Dssp takes significantly
>> less time to do the calculations, however compared to Pymol
>> dot_density of 3, the areas sometimes differ by 4,5,6,  squared
>> angstroms!
>>
>> Any comment on that?
>>
>> 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...

I would appreciate any help regarding this.

On Tue, Apr 25, 2017 at 12:36 PM, Ahmad Abdelzaher
<und...@gm...> wrote:
> Hello,
>
> Does the get_area command use the rolling ball algorithm? Which
> dot_density corresponds to the best accuracy 1 or 4? Is there a reason
> why it consumes more time to compute sasa? Dssp takes significantly
> less time to do the calculations, however compared to Pymol
> dot_density of 3, the areas sometimes differ by 4,5,6,  squared
> angstroms!
>
> Any comment on that?
>
> Regards.

Hello,

Does the get_area command use the rolling ball algorithm? Which
dot_density corresponds to the best accuracy 1 or 4? Is there a reason
why it consumes more time to compute sasa? Dssp takes significantly
less time to do the calculations, however compared to Pymol
dot_density of 3, the areas sometimes differ by 4,5,6,  squared
angstroms!

Any comment on that?

Regards.

Wow!
I haven't seen so many options before, even after installing Edu PyMOL
correctly.

Do you all of you get these options (Win10 users)?
I only get to see
PyMOL + Tcl-tk, and,
PyMOL + Tcl-tk + Console.

AJ, did you install anything extra?
This may seem another dumb question, but your answers will be helpful.

Regards
Dheeraj

I think Tcl-Tk GUI + Console is the most familiar pymol.

Jordan

> On Apr 21, 2017, at 3:06 PM, Jed Goldstone <jgo...@wh...> wrote:
> 
> The 3D stuff (Zalman, etc) is only if you're using 3D glasses. I typically use the Tk + console option that opens two windows (the GUI and a pythonesque console).
> 
> Jed
> 
> On Apr 21, 2017 2:16 PM, "AJ Vincelli" <ajv...@gm... <mailto:ajv...@gm...>> wrote:
> Hello all,
> 
> I hate to ask a dumb question, but I need some seriously novice help. I just installed educational-use-only PyMOL (version 1.7.4.5, x64) on a WIndows 10 machine, and I'm trying to open the program from the Windows 10 start menu. However, there are many choices! Does anybody know what the difference is between these options (like Tcl-Tk, Console, Quad buffer, Dynamic, etc.)? Or is there a handy webpage that explains the difference? I can't find anything in the Wiki or FAQ websites.
> 
> Screenshot is attached and embedded here:
> 
> <PyMOL Options.png>
> 
> Thanks!
> 
> AJ
> 
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot <" rel="nofollow">http://sdm.link/slashdot>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users <" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users>
> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
> ------------------------------------------------------------------------------
> 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...

The 3D stuff (Zalman, etc) is only if you're using 3D glasses. I typically
use the Tk + console option that opens two windows (the GUI and a
pythonesque console).

Jed

On Apr 21, 2017 2:16 PM, "AJ Vincelli" <ajv...@gm...> wrote:

> Hello all,
>
> I hate to ask a dumb question, but I need some seriously novice help. I
> just installed educational-use-only PyMOL (version 1.7.4.5, x64) on a
> WIndows 10 machine, and I'm trying to open the program from the Windows 10
> start menu. However, there are many choices! Does anybody know what the
> difference is between these options (like Tcl-Tk, Console, Quad buffer,
> Dynamic, etc.)? Or is there a handy webpage that explains the difference? I
> can't find anything in the Wiki or FAQ websites.
>
> Screenshot is attached and embedded here:
>
>
> Thanks!
>
> AJ
>
>
> ------------------------------------------------------------
> ------------------
> 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...
>

That's not a dumb question AJ. I have been using Pymol for a while and I
haven't got a clue. :D

On Fri, Apr 21, 2017 at 8:15 PM, AJ Vincelli <ajv...@gm...> wrote:

> Hello all,
>
> I hate to ask a dumb question, but I need some seriously novice help. I
> just installed educational-use-only PyMOL (version 1.7.4.5, x64) on a
> WIndows 10 machine, and I'm trying to open the program from the Windows 10
> start menu. However, there are many choices! Does anybody know what the
> difference is between these options (like Tcl-Tk, Console, Quad buffer,
> Dynamic, etc.)? Or is there a handy webpage that explains the difference? I
> can't find anything in the Wiki or FAQ websites.
>
> Screenshot is attached and embedded here:
>
>
> Thanks!
>
> AJ
>
>
> ------------------------------------------------------------
> ------------------
> 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...
>

Hello all,

I hate to ask a dumb question, but I need some seriously novice help. I 
just installed educational-use-only PyMOL (version 1.7.4.5, x64) on a 
WIndows 10 machine, and I'm trying to open the program from the Windows 
10 start menu. However, there are many choices! Does anybody know what 
the difference is between these options (like Tcl-Tk, Console, Quad 
buffer, Dynamic, etc.)? Or is there a handy webpage that explains the 
difference? I can't find anything in the Wiki or FAQ websites.

Screenshot is attached and embedded here:


Thanks!

AJ

The usual cause is that some backbone atoms for those residues are missing or misnamed. There are also some more exotic possibilities but I'd have to look at the file to know. 

One possibility is to tell pymol to draw dotted lines for regions without atoms:

set cartoon_gap_cutoff, 20

Cheers,
-Spencer
On April 13, 2017 at 10:58:48, 阿毅 (yn...@12...) wrote:

Hi,

I use pymol for display the structures of protein.
I meet a problem on showing at the cartoon style.
Some residues are not show in cartoon.
like this



How can I fix it?
Thanks.
Looking forward your reply.

Li Yi

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Dear Colleagues,
The deadline for application to the annual CCP4/APS school in macromolecular crystallography: “From data collection to structure refinement and beyond” is in less than a week - April 19.
Please read the thread below for basic information on the school.
For all details, please visit http://www.ccp4.ac.uk/schools/APS-2017/index.php

With regards,
Garib, Ronan and Nukri


Ruslan Sanishvili (Nukri), Ph.D.
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Lemont, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsa...@an...

________________________________
From: Sanishvili, Ruslan [rsa...@an...]
Sent: Monday, March 27, 2017 3:16 PM
To: pym...@li...
Subject: [PyMOL] REMINDER: 10th CCP4/APS Crystallographic School in the USA

Dear Colleagues,

This is a friendly reminder for the 10th annual CCP4 crystallographic school “From data collection to structure refinement and beyond”, held from June 16 to 26 at Advanced Photon Source (APS), Argonne National Laboratory (ANL). If you are interested attending, please take a look at the original announcement below for more details. For all details, please visit the school web site http://www.ccp4.ac.uk/schools/APS-2017/index.php


With best wishes,
Garib, Ronan and Nukri

Ruslan Sanishvili (Nukri), Ph.D.
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Lemont, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsa...@an...

________________________________
From: Sanishvili, Ruslan
Sent: Wednesday, February 01, 2017 2:57 PM
To: pym...@li...
Subject: 10th CCP4/APS Crystallographic School in the USA

Dear Colleagues,

We are pleased to announce the 10th annual CCP4 crystallographic school “>From data collection to structure refinement and beyond”, held at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2017/index.php

Dates: June 19 through 26, 2017

Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA

The school comprises
Data collection workshop: beamline training; data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors, respectively; and data processing. For data collection, only the participants' crystals will be used.
Crystallographic computation workshop: will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on, interactive trouble-shooting of the technical difficulties the participants face in their projects. We have had considerable success resolving these problems in past years, attested by resulting publications http://www.ccp4.ac.uk/schools/APS-school/publications.php

Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops.

Application: Application deadline is April 19. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2017/index.php

Registration fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation, lodging and breakfast. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses.

We hope to see you at the school.
Garib, Ronan and Nukri


Ruslan Sanishvili (Nukri), Ph.D.
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Lemont, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsa...@an...

> 
> -- 
> Jo?o M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
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> 
> Message: 3
> Date: Thu, 13 Apr 2017 10:03:20 +0800 (GMT+08:00)
> From: ?? <yn...@12...>
> Subject: [PyMOL] pymol: residues not show in cartoon
> To: pymol-users <pym...@li...>
> Message-ID: <4ae...@12...>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi,
> 
> 
> I use pymol for display the structures of protein.
> I meet a problem on showing at the cartoon style.
> Some residues are not show in cartoon.
> like this
> 
> 
> How can I fix it?
> Thanks.
> Looking forward your reply.
> 
> 
> Li Yi

I can’t see your example, but to find out you have to look at your coordinate file:
Either there are unresolved residues (missing in the coordinate file, most frequently in loop regions),
In this case you have to look for a coordinate file that is more complete

or there are posttranslational modification, and these residues are present in the coordinate file as HETATM records,
These would show up with “show spheres, organic” 

Annemarie

Hi,


I use pymol for display the structures of protein.
I meet a problem on showing at the cartoon style.
Some residues are not show in cartoon.
like this


How can I fix it?
Thanks.
Looking forward your reply.


Li Yi

Thanks for the tips Thomas. I will try and let you know.

João

On Tue, Apr 11, 2017 at 9:12 PM, Thomas Holder <
tho...@sc...> wrote:

> Hi João,
>
> Before diving into the hassle of installing additional compilers (which
> probably won't make a difference) I recommend to get familiar with a
> debugger like gdb and obtain a stack trace of the crash.
>
> To compile PyMOL with debug symbols, do
>
> export DEBUG=1
>
> before running setup.py. Then run PyMOL (actually: python) with gdb. There
> is a bit of a learning curve to get familiar with gdb, but considering that
> you already spend time on this problem and are willing to spend more, I
> think it's worthwhile.
>
> Cheers,
>   Thomas
>
> On 11 Apr 2017, at 19:08, João M. Damas <jm...@it...> wrote:
>
> > Thanks for the feedback, Folmer!
> >
> > I am using CentOS. I already used --use-msgpackc=no and it did not
> improve. gcc --version gives me 4.8.5 (I cannot update more). Do you think
> it would be worth it to install gcc 4.9? On the install page there was said
> that a regression to 4.4 could work, but I don’t know.
> >
> > Anyone else using CentOS having problems with pymol installation?
> >
> > Thanks,
> > João
> >
> >
> > On Wed, Mar 29, 2017 at 10:35 AM, Folmer Fredslund <fo...@gm...>
> wrote:
> > Hi João,
> >
> > On Ubuntu 16.04 (you didn't mention what you were running) with gcc-4.9
> and "--use-msgpackc=no" I get a working pymol with revision 4170.
> >
> > Have you tried creating a new user and test pymol from that account?
> That should help you identify if it is solely a problem with your own
> account.
> >
> > HTH,
> > Folmer
> >
> >
> > On 2017-03-28 03:15, João M. Damas wrote:
> >> Nobody experiencing the same issues? Any tips on what I may be doing
> wrong on the installation?
> >>
> >> João
> >>
> >> On Fri, Mar 17, 2017 at 4:08 PM, João M. Damas <jm...@it...>
> wrote:
> >> Dear all,
> >>
> >> I started experiencing segmentation fault on a pymol that I had
> installed through the omnia channel on conda.
> >>
> >> Then, I decided to install from scratch using this recipe:
> https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN
> >>
> >> Still getting the segmentation fault, so maybe something changed in my
> system and it's conflicting with?
> >>
> >> The segmentation fault is not on launching PyMOL, but rather when I do
> stuff: loading a PDB file, building a fragment. Like this:
> >>
> >> ```
> >> ./pymol: line 3: 28505 Segmentation fault      "/usr/bin/python2.7"
> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
> >> ```
> >>
> >> Curiously, when I load a 1.740 session (.pse file I had saved), it
> works (no segmentation fault), I can even perform commands like select and
> stuff, and they work. If I load a more recent 1.803 session, it also seg
> faults:
> >>
> >> ```
> >>  Executive: Loading version 1.803 session...
> >> ./pymol: line 3: 29221 Segmentation fault      "/usr/bin/python2.7"
> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
> >> ```
> >>
> >> Any clues? Am I doing something wrong?
> >>
> >> Thanks,
> >> João
> >>
> >> --
> >> João M. Damas
> >> PhD Student
> >> Protein Modelling Group
> >> ITQB-UNL, Oeiras, Portugal
> >> Tel:+351-214469613
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>


-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613

Hej Raag,

my name is Andreas and I wrote PyTMs back for my PhD. It essentially uses
PyMOLs basic editing functions to build PTMs onto protein models.
PyTMs is a simple tool and has its clear restrictions, but generally it is
nice to play around with and explore hypotheses with.

The challenge is that drawing conclusions about the impact of PTM on
tertiary structure is very limited and that there will be increasing
uncertainty about positioning of atoms the larger the PTM is. Also charge
effects are an issue and overall one will increasingly be confronted
with questions regarding Molecular Dynamics.

As far as your project is concerned you can rather easily add a Tyrosine
(or custom fragments) using the builder in PyMOL:
https://pymolwiki.org/index.php/Modeling_and_Editing_Structures

In editing mode, you can select an atom to extend on and manually select:
*build-->residue *from the menu

Additionally I'd also point out the API command to experiment with:
editor.attach_amino_acid("pk1","tyr")

If you have any questions about the editing or PyTMs feel free to PM me.
Unfortunately, I can't promise to update the plugin unless I find the spare
time to invest.

Cheers,

Andreas

On Wed, Apr 12, 2017 at 9:36 AM, Raag Saluja <sal...@gm...> wrote:

> Hi!
>
> PyTMs is wonderful and permits me to really play around with a lot of
> different PTMs!
>
> In PyTMs, I can find some of the PTMs that I need to work on (acetylation
> and phosphorylation) for my PhD. However, there are some PTMs that I need
> to work on for my PhD, but I can't find those features in PyTMs. I need to
> study (1) tyrosination/detyrosination, polyglutamylation and
> polyglycylation and (2) PTMs on the C-termini. How do I go about those?
>
> This might sound like I'm asking too much, but can you please include
> these in PyTMs as well? PyTMs is really user friendly. It would be
> wonderful if you can please do that!
>
> Regards,
> Raag
>
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>

Hi!

PyTMs is wonderful and permits me to really play around with a lot of
different PTMs!

In PyTMs, I can find some of the PTMs that I need to work on (acetylation
and phosphorylation) for my PhD. However, there are some PTMs that I need
to work on for my PhD, but I can't find those features in PyTMs. I need to
study (1) tyrosination/detyrosination, polyglutamylation and
polyglycylation and (2) PTMs on the C-termini. How do I go about those?

This might sound like I'm asking too much, but can you please include these
in PyTMs as well? PyTMs is really user friendly. It would be wonderful if
you can please do that!

Regards,
Raag

Hi Raag,

You need to run MacPyMOL with the "X11 Hybrid" interface, see:

https://pymolwiki.org/index.php/MAC_Install#X11_Hybrid

Cheers,
  Thomas

On 12 Apr 2017, at 08:02, Raag Saluja <sal...@gm...> wrote:

> Hi!
> 
> I needed to install PyTMs but am unable to do so. I can't find the plugin manager. In the menu, after the wizard I have 'help' not 'plugins'.
> 
> I installed the educational version of MacPyMOL in around Aug/Sep 2015.
> 
> Looking forward to your help,
> Regards,
> Raag

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi!

I needed to install PyTMs but am unable to do so. I can't find the plugin
manager. In the menu, after the wizard I have 'help' not 'plugins'.

I installed the educational version of MacPyMOL in around Aug/Sep 2015.

Looking forward to your help,
Regards,
Raag