pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Clarisa,

You can pass "width" and "height" arguments to the "mpng" command, like this:

  mpng fileprefix, width=720, height=480

See also https://pymolwiki.org/index.php/mpng

Hope that helps.

Cheers,
  Thomas

> On Jan 29, 2019, at 5:47 PM, Clarisa Alvarez <cla...@gm...> wrote:
> 
> Could anyone help me how i could change resolution of my png images make to perform a video, that changes resolution when i open with movie maer.
> Thanks in advance.
> Clarisa.

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

> On Jan 30, 2019, at 06:00, pym...@li... wrote:
> 
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> Today's Topics:
> 
>   1. pymol movie help (Clarisa Alvarez)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 29 Jan 2019 13:47:27 -0300
> From: Clarisa Alvarez <cla...@gm...>
> To: pym...@li...
> Subject: [PyMOL] pymol movie help
> Message-ID:
> 	<CAF...@ma...>
> Content-Type: text/plain; charset="utf-8"
> 
> Could anyone help me how i could change resolution of my png images make to
> perform a video, that changes resolution when i open with movie maer.
> Thanks in advance.
> Clarisa.
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Could anyone help me how i could change resolution of my png images make to
perform a video, that changes resolution when i open with movie maer.
Thanks in advance.
Clarisa.

Hi Nathan,

If you have access to pip2 (from python2), you can install python2 version
of PyMol. I've just done tried this on my computer with conda and python2
and it worked fine.

Hope this helps, Mat

On Mon, Jan 28, 2019 at 6:44 PM Nathan Guerin <ng...@cs...> wrote:

> Hello,
>
> I use Fedora 29 and have installed the latest packaged version of pymol
> (2.1.0).  This seems to run, by default, on Python 3, at least on later
> versions of Fedora.  Is there any way to configure which python
> interpreter to use at runtime?  I have some Python 2 plugins that I
> would like to be able to use, but since there are breaking syntax
> changes between 2 and 3, the scripts don't work anymore.
>
> Any thoughts?
>
> Thank you!
> Nate Guerin
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

Hello,

I use Fedora 29 and have installed the latest packaged version of pymol
(2.1.0).  This seems to run, by default, on Python 3, at least on later
versions of Fedora.  Is there any way to configure which python
interpreter to use at runtime?  I have some Python 2 plugins that I
would like to be able to use, but since there are breaking syntax
changes between 2 and 3, the scripts don't work anymore.

Any thoughts?

Thank you!
Nate Guerin

> 
> Message: 1
> Date: Thu, 17 Jan 2019 09:53:34 -0300
> From: Clarisa Alvarez <cla...@gm...>
> To: pym...@li...
> Subject: Re: [PyMOL] PyMOL-users Digest, Vol 152, Issue 2
> Message-ID:
> 	<CAF...@ma...>
> Content-Type: text/plain; charset="utf-8"
> 
> Hello
> How i could set in pymol to see electrostatic coloring of a surface in an
> easy way?
> Thanks in advance,
> Clarisa.
> 
> El jue., 17 ene. 2019 a las 9:00, <pym...@li...>
> escribi?:


Hi Clarisa
You use the ABPS plugin, see: https://pymolwiki.org/index.php/APBS
Annemarie
____________________________________________________________

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     

Hello
How i could set in pymol to see electrostatic coloring of a surface in an
easy way?
Thanks in advance,
Clarisa.

El jue., 17 ene. 2019 a las 9:00, <pym...@li...>
escribió:

> Send PyMOL-users mailing list submissions to
>         pym...@li...
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
>         pym...@li...
>
> You can reach the person managing the list at
>         pym...@li...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
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>
> Today's Topics:
>
>    1. [MGMS-DS]: Molecular Modelling Workshop + Tim Clark Birthday
>       Symposium: April 08-11, 2019 in Erlangen, Germany (Harald Lanig)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 17 Jan 2019 09:40:25 +0100
> From: Harald Lanig <har...@fa...>
> To: <pym...@li...>
> Subject: [PyMOL] [MGMS-DS]: Molecular Modelling Workshop + Tim Clark
>         Birthday Symposium: April 08-11, 2019 in Erlangen, Germany
> Message-ID: <c44...@fa...>
> Content-Type: text/plain; charset="utf-8"; format=flowed
>
> Dear list subscribers,
>
> we are very delighted to announce this year?s ?33rd Molecular Modelling
> Workshop (MMWS)? (http://mmws2019.mgms-ds.de) that takes place on April,
> Monday 8th to Wednesday 10th, 2019, at the
> Friedrich-Alexander-University in Erlangen, Germany.
>
> The MMWS has a long history of giving young scientists (especially
> graduate students) the opportunity to present their work and dive into
> discussions with each other and the "older experts" of the field to gain
> valuable feedback from academic as well as industrial colleagues. Oral
> and poster contributions are welcome from all areas of molecular
> modelling ? from the life sciences, computational biology and chemistry,
> cheminformatics, to materials sciences.
>
> Starting with the scientific program on Monday after lunch should allow
> to avoid travelling on weekend keeping the expenses at a minimum. A
> hearty workshop dinner and a traditional joint evening in Erlangen?s
> Steinbach-Br?u brewery complement the scientific program. The workshop
> is organised by the German Section of the Molecular Graphics and
> Modelling Society (MGMS-DS e.V.).
>
> ####### Satellite symposium in honour of Tim Clark's 70th birthday #######
> Directly after the MMWS, there will be a one-day symposium on Thursday
> April 11th, 2019 to celebrate the occasion of Tim Clark's 70th birthday.
> You are invited to attend this meeting and extend your stay in Erlangen
> by an extra day. There will be invited lectures only and no contributed
> talks. There is no registration, conference desk, or extra fee.
> Nevertheless, we expect that you indicate your interest in attending on
> Thursday by checking the corresponding field during registration for the
> MMWS.
> For further information about our Birthday Symposium, please refer to
> "Tim-Clark-Day" via https://mmws2019.mgms-ds.de/index.php?m=113
>
> ####### Pre-conference workshop #######
> For the second time at our Molecular Modeling Workshop, Schr?dinger is
> offering a pre-conference workshop entiteled "Structure-based Drug
> Design using the Schr?dinger Suite". If you are interested in
> participating at the software session, please checkmark the
> corresponding field upon filling the registration form.
>
> ####### Plenary Speakers #######
> We are very happy to announce that four outstanding researchers accepted
> our invitation to present a plenary lecture at the Modeling workshop:
>
> Matthias Bremer (Merck KGaA, Darmstadt)
> "The Role of Quantum Chemistry in the Development of Liquid Crystals for
> Display Applications"
>
> Ruth Brenk (University of Bergen)
> "Structure-based design of riboswitch ligands and selective NMT inhibitors"
>
> Bernd Meyer (University of Erlangen)
> "Chemistry at the solid-liquid interface"
>
> Rochus Schmid (Ruhr-University Bochum)
> "Force fields for porous coordination polymers - a tricky business"
>
> ####### Poster and Lecture Awards #######
> As in the past years, there will be two poster awards of EUR 100 each
> and three lecture awards for the best contributed oral presentations:
>
> 1st winner: Travel bursary to attend the Young Modeller's Forum in
> London, UK, plus a speaker slot option at YMF (travel expenses are
> reimbursed up to EUR 500)
>
> 2nd winner: EUR 200 travel expenses reimbursement
>
> 3rd winner: EUR 100 travel expenses reimbursement
>
> Only undergraduate and graduate research students qualify for the poster
> and lecture awards.
>
> ####### Registration and poster/talk submission #######
> Submit talks and/or poster titles via the registration form accessible
> on the workshop website https://mmws2019.mgms-ds.de/index.php?m=register
> The deadline for all submissions is February 22nd, 2019.
>
> ####### General information #######
> Website http://mmws2019.mgms-ds.de will provide all necessary
> information about the meeting.
>
> We are looking forward to meeting you in Erlangen!
> - Paul Czodrowski, Scientific Committee Workshop Organisation 2019
> - Harald Lanig, Chairman of the MGMS-DS e.V. (http://www.mgms-ds.de)
>
> --
> ------------------------------------------------------------------------
>   PD Dr. Harald Lanig       Universitaet Erlangen/Nuernberg
>   Zentralinstitut fuer Scientific Computing (ZISC)
>   Geschaeftsfuehrer         Martensstrasse 5a, 91058 Erlangen
>
>   Fon   +49 9131-85 20781   har...@fa...
>   Fax   +49 9131-85 20785   http://www.zisc.uni-erlangen.de
> ------------------------------------------------------------------------
>
>
>
>
> ------------------------------
>
>
>
> ------------------------------
>
> 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 152, Issue 2
> *******************************************
>

Dear list subscribers,

we are very delighted to announce this year’s “33rd Molecular Modelling 
Workshop (MMWS)” (http://mmws2019.mgms-ds.de) that takes place on April, 
Monday 8th to Wednesday 10th, 2019, at the 
Friedrich-Alexander-University in Erlangen, Germany.

The MMWS has a long history of giving young scientists (especially 
graduate students) the opportunity to present their work and dive into 
discussions with each other and the "older experts" of the field to gain 
valuable feedback from academic as well as industrial colleagues. Oral 
and poster contributions are welcome from all areas of molecular 
modelling – from the life sciences, computational biology and chemistry, 
cheminformatics, to materials sciences.

Starting with the scientific program on Monday after lunch should allow 
to avoid travelling on weekend keeping the expenses at a minimum. A 
hearty workshop dinner and a traditional joint evening in Erlangen’s 
Steinbach-Bräu brewery complement the scientific program. The workshop 
is organised by the German Section of the Molecular Graphics and 
Modelling Society (MGMS-DS e.V.).

####### Satellite symposium in honour of Tim Clark's 70th birthday #######
Directly after the MMWS, there will be a one-day symposium on Thursday 
April 11th, 2019 to celebrate the occasion of Tim Clark's 70th birthday. 
You are invited to attend this meeting and extend your stay in Erlangen 
by an extra day. There will be invited lectures only and no contributed 
talks. There is no registration, conference desk, or extra fee. 
Nevertheless, we expect that you indicate your interest in attending on 
Thursday by checking the corresponding field during registration for the 
MMWS.
For further information about our Birthday Symposium, please refer to 
"Tim-Clark-Day" via https://mmws2019.mgms-ds.de/index.php?m=113

####### Pre-conference workshop #######
For the second time at our Molecular Modeling Workshop, Schrödinger is 
offering a pre-conference workshop entiteled "Structure-based Drug 
Design using the Schrödinger Suite". If you are interested in 
participating at the software session, please checkmark the 
corresponding field upon filling the registration form.

####### Plenary Speakers #######
We are very happy to announce that four outstanding researchers accepted 
our invitation to present a plenary lecture at the Modeling workshop:

Matthias Bremer (Merck KGaA, Darmstadt)
"The Role of Quantum Chemistry in the Development of Liquid Crystals for 
Display Applications"

Ruth Brenk (University of Bergen)
"Structure-based design of riboswitch ligands and selective NMT inhibitors"

Bernd Meyer (University of Erlangen)
"Chemistry at the solid-liquid interface"

Rochus Schmid (Ruhr-University Bochum)
"Force fields for porous coordination polymers - a tricky business"

####### Poster and Lecture Awards #######
As in the past years, there will be two poster awards of EUR 100 each 
and three lecture awards for the best contributed oral presentations:

1st winner: Travel bursary to attend the Young Modeller's Forum in 
London, UK, plus a speaker slot option at YMF (travel expenses are 
reimbursed up to EUR 500)

2nd winner: EUR 200 travel expenses reimbursement

3rd winner: EUR 100 travel expenses reimbursement

Only undergraduate and graduate research students qualify for the poster 
and lecture awards.

####### Registration and poster/talk submission #######
Submit talks and/or poster titles via the registration form accessible 
on the workshop website https://mmws2019.mgms-ds.de/index.php?m=register
The deadline for all submissions is February 22nd, 2019.

####### General information #######
Website http://mmws2019.mgms-ds.de will provide all necessary 
information about the meeting.

We are looking forward to meeting you in Erlangen!
- Paul Czodrowski, Scientific Committee Workshop Organisation 2019
- Harald Lanig, Chairman of the MGMS-DS e.V. (http://www.mgms-ds.de)

-- 
------------------------------------------------------------------------
  PD Dr. Harald Lanig       Universitaet Erlangen/Nuernberg
  Zentralinstitut fuer Scientific Computing (ZISC)
  Geschaeftsfuehrer         Martensstrasse 5a, 91058 Erlangen

  Fon   +49 9131-85 20781   har...@fa...
  Fax   +49 9131-85 20785   http://www.zisc.uni-erlangen.de
------------------------------------------------------------------------

Dear Colleagues,

We are pleased to announce the 12th annual CCP4 crystallographic school “From data collection to structure refinement and beyond” will be held on June 17-24, 2019 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2019/index.php.

Dates: June 17 through 24, 2019

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

The school comprises two parts: data collection workshop and crystallographic computing workshop. Data collection workshop includes 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 (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website.

Applicants: Graduate students, postdoctoral researchers and early-career faculty, 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 15th, 2019. To apply, visit https://www.ccp4.ac.uk/schools/APS-2019/application.php.

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 and lodging. The workshop organizers can assist in making the lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals).

We hope to see you at the school.

Charles, Garib and Qingping