pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] PyMOL 2.3 released

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

Greetings,

We are happy to announce the release of PyMOL 2.3. Download ready-to-use bundles from https://pymol.org/ or update your installation with "conda install -c schrodinger pymol".

New features include:
- Atom-level cartoon transparency
- Fast MMTF export
- Sequence viewer gaps display

This is the first time that we provide PyMOL bundles with Python 3. If you use custom or third-party Python 2 scripts, they might stop working until you convert them (e.g. using a converter tool like 2to3).

Find the complete release notes at:
https://pymol.org/d/media:new23 

We welcome any feedback and bug reports.

Cheers,
- The PyMOL Team at Schrödinger

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] PyMOL command line scripts

[Neena S. E. <nee...@gm...>]

Hi Manish,

Thank you for building these amazing scripts! However, I was wondering how
to install these scripts into Pymol. I tried copying the URL for
PhiPsiAngles code in the Plugin manager of Pymol, however the plugin is not
being installed. Please advise.

Many thanks,
Neena

On Thu, 7 Feb 2019 at 05:45, Manish Sud <ms...@sa...> wrote:

> Hi All,
>
> I'll like to share with you the availability of the following new command
> line scripts:
>
> o PyMOLCalculatePhiPsiAngles.py
> o PyMOLGenerateRamachandranPlots.py
> o PyMOLMutateAminoAcids.py
> o PyMOLMutateNucleicAcids.py
> o PyMOLVisualizeCavities.py
> o PyMOLVisualizeInterfaces.py
> o PyMOLVisualizeSurfaceAndBuriedResidues.py
>
> These scripts are distributed as part of MayaChemTools. The scripts have
> been tested using the open source release of PyMOL available for both
> Python2 and Python3.
>
> Please visit http://www.MayaChemTools.org for additional details.
>
> Thanks,
> Manish
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Reference point shifts when display screen is changed

[Gyanendra K. <gya...@bm...>]

Hi there,

I am facing this problem of the reference point moving to a corner of the display window when I unplug the external monitor and the display moves to the MacBook screen, or when I connect another display e.g. a TV screen.
Reset command or re-centering on an atom does not fix the problem and I end up closing pymol and having to restart the program.

Has anybody faced this problem and found a solution?

I am running pymol on MacOS Sierra Version 10.12.6. MacBook Pro 2017.

Thanks,
Gyan




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[PyMOL] PyMOL command line scripts

[Manish S. <ms...@sa...>]

Hi All,
I'll like to share with you the availability of the following new
command line scripts:
o PyMOLCalculatePhiPsiAngles.pyo PyMOLGenerateRamachandranPlots.pyo
PyMOLMutateAminoAcids.pyo PyMOLMutateNucleicAcids.pyo
PyMOLVisualizeCavities.pyo PyMOLVisualizeInterfaces.pyo
PyMOLVisualizeSurfaceAndBuriedResidues.py
These scripts are distributed as part of MayaChemTools. The scripts
have been tested using the open source release of PyMOL available for
both Python2 and Python3.
Please visit http://www.MayaChemTools.org for additional details.
Thanks,Manish

Re: [PyMOL] pymol movie help

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

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.

Re: [PyMOL] PyMOL-users Digest, Vol 152, Issue 6

[Len B. <ban...@um...>]

> On Jan 30, 2019, at 06:00, pym...@li... wrote:
> 
> 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..."
> 
> 
> 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:
> 	<CAFTZvua5GPmVDXeYFKeaYh-aHkum2A=Cro...@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.
> -------------- next part --------------
> An HTML attachment was scrubbed...
> 
> ------------------------------
> 
> 
> 
> ------------------------------
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> Subject: Digest Footer
> 
> _______________________________________________
> PyMOL-users mailing list
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> End of PyMOL-users Digest, Vol 152, Issue 6
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[PyMOL] pymol movie help

[Clarisa A. <cla...@gm...>]

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.

Re: [PyMOL] How can I choose which Python interpreter to use?

[Mateusz B. <bie...@gm...>]

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
>

[PyMOL] How can I choose which Python interpreter to use?

[Nathan G. <ng...@cs...>]

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

Re: [PyMOL] PyMOL-users Digest, Vol 152, Issue 3

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

> 
> 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     

Re: [PyMOL] PyMOL-users Digest, Vol 152, Issue 2

[Clarisa A. <cla...@gm...>]

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..."
>
>
> 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
> *******************************************
>

[PyMOL] [MGMS-DS]: Molecular Modelling Workshop + Tim Clark Birthday Symposium: April 08-11, 2019 in Erlangen, Germany

[Harald L. <har...@fa...>]

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

[PyMOL] 12th CCP4/APS Crystallographic School in the US

[Xu, Q. <qx...@an...>]

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

Re: [PyMOL] Super and Align missing residues

[Nathan C. <ncl...@cs...>]

For anyone who has found this thread, I've taken some time and put together
an alignment + RMSD script for Pymol (using BioPython). You can find it on
GitHub, here <https://github.com/nclement/cvc-scripts/tree/master/alignment>
.
It's a bit overkill, and only handles single chain proteins, but it's quite
robust if it fits your needs.

On Wed, Jul 4, 2018 at 3:05 PM Thomas Holder <tho...@sc...>
wrote:

> Hi Nathan,
>
> I have some insights for this issue. Basically the long gaps between the
> selected parts become too expensive in the alignment scoring. Changing e.g.
> the gap extension penalty leads to the expected result:
>
> # default is extend=-0.7, lowering to -0.6
> super gold & contact_all, test, cycles=0, object=super, extend=-0.6
>
> I think PyMOL's handling of selection gaps during the alignment could be
> improved, they should be handled different from regular alignment gaps.
>
> Cheers,
>   Thomas
>
> > On Jun 28, 2018, at 2:14 PM, Thomas Holder <
> tho...@sc...> wrote:
> >
> > Hi Nathan,
> >
> > Thank you very much for the files and instructions. I can reproduce the
> problem. I haven't seen this before and don't know yet what's going wrong,
> we will investigate.
> >
> > Cheers,
> >  Thomas
> >
> >> On Jun 28, 2018, at 10:50 AM, ncl...@cs... wrote:
> >>
> >> The alignment in this example is nearly perfect. Even the residues left
> >> out of the fitting have perfect matches at the sequence level (as can be
> >> seen by saving the super object and turning on the sequence alignment
> and
> >> contact_all).
> >>
> >> PyMOL>load 1AY7_u.pdb, test
> >> CmdLoad: "1AY7_u.pdb" loaded as "test".
> >> PyMOL>load 1AY7_b.pdb, gold
> >> CmdLoad: "1AY7_b.pdb" loaded as "gold".
> >> PyMOL>select contact_rec, gold & chain R & (all within 10 of gold &
> chain
> >> L) & n. ca
> >> Selector: selection "contact_rec" defined with 33 atoms.
> >> PyMOL>select contact_lig, gold & chain L & (all within 10 of gold &
> chain
> >> R) & n. ca
> >> Selector: selection "contact_lig" defined with 33 atoms.
> >> PyMOL>select contact_all, contact_rec + contact_lig
> >> Selector: selection "contact_all" defined with 66 atoms.
> >> PyMOL>super gold & contact_all, test, cycles=0
> >> MatchAlign: aligning residues (66 vs 185)...
> >> MatchAlign: score 143.882
> >> ExecutiveAlign: 58 atoms aligned.
> >> Executive: RMS =    0.524 (58 to 58 atoms)
> >>
> >> <1AY7_u.pdb><1AY7_b.pdb>
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Re: [PyMOL] Artificial Lines for Sticks

[Jarrett J. <jar...@sc...>]

Hi Michel,

By chance can you attach an example image?

Thanks,
Jarrett J.

On Mon, Dec 17, 2018 at 11:52 AM Michel Rickhaus <mic...@gm...>
wrote:

> Hi all
>
> Did anyone else note that rendering sticks on high resolution with
> ray_trace_mode, 1 yields black lines down the middle of the sticks in some
> instances? I guess its where the cylinder meets up.
> Any idea how to prevent this? It's quite annoying to remove the manually
> in an image editor after
>
> Cheers
> Michel
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 
Jarrett Johnson
PyMOL Developer
Schrödinger, Inc.

[PyMOL] Artificial Lines for Sticks

[Michel R. <mic...@gm...>]

Hi all

Did anyone else note that rendering sticks on high resolution with
ray_trace_mode, 1 yields black lines down the middle of the sticks in some
instances? I guess its where the cylinder meets up.
Any idea how to prevent this? It's quite annoying to remove the manually in
an image editor after

Cheers
Michel

Re: [PyMOL] Change appearance of CGO Objects

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

Hi Michel,

Some operations should be compatible with the "color" command, in particular all BEGIN/END operations, as long as there is no COLOR operation. Only those which have the color as part of the operation arguments (like CYLINDER and TRIANGLE) won't be recolorable.

Example:

from pymol import cgo, cmd
obj = [
   cgo.BEGIN, cgo.TRIANGLES,
   cgo.VERTEX, 0.0, 0.0, 0.0,
   cgo.VERTEX, 1.0, 0.0, 0.0,
   cgo.VERTEX, 0.0, 1.0, 0.0,
   cgo.END
   ]
cmd.load_cgo(obj, 'foo')
cmd.color('blue', 'foo') 

Cheers,
  Thomas

> On Dec 17, 2018, at 3:06 PM, Michel Rickhaus <mic...@gm...> wrote:
> 
> Hi all
> 
> I was wondering whether it is possible to change the appearance of a CGO Object after creation. I typically set the attributes of each CGO (plane for instance) using 
> 
> dict = {'ALPHA':1.0, 'COLOR':[0.99, 0.87, 0.67], 'INVERT':False} 
> 
> before the creating of the CGO and calling dict. Sometimes I'd like to change these after creation. The typical PyMol commands (color..) do not seem to work. If I dont set transparency using dict, i can use set cgo_transparency later. The same does not work for color (there is no set cgo_color or related...)
> It seems to have been asked in part before (https://www.mail-archive.com/pym...@li.../msg08330.html)
> 
> 
> Any help is appreciated
> 
> Michel

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] Change appearance of CGO Objects

[Michel R. <mic...@gm...>]

Hi all

I was wondering whether it is possible to change the appearance of a CGO
Object after creation. I typically set the attributes of each CGO (plane
for instance) using

dict = {'ALPHA':1.0, 'COLOR':[0.99, 0.87, 0.67], 'INVERT':False}

before the creating of the CGO and calling dict. Sometimes I'd like to
change these after creation. The typical PyMol commands (color..) do not
seem to work. If I dont set transparency using dict, i can use set
cgo_transparency later. The same does not work for color (there is no set
cgo_color or related...)
It seems to have been asked in part before (
https://www.mail-archive.com/pym...@li.../msg08330.html
)


Any help is appreciated

Michel

Re: [PyMOL] how to make selected residues blurry?

[Jared S. <jar...@co...>]

Hi Yeping -  

The `set_view` command sets the view matrix for the camera in PyMOL. Once you have the view you want set up in the viewport, you can copy the matrix to the system clipboard using the “Get View” button in the top GUI window and paste it into your .pml script, or print it to the console by using the `get_view` command.  

Hope that helps.  

Cheers,  
Jared


On December 9, 2018 at 10:40:52 AM, sunyeping (sun...@al...(mailto:sun...@al...)) wrote:

> Hi Jared,
>  
> Your solution is very clever and helpful, but I don't know how to use the set_view command. I think it is vey important here because after this setting the scene becomes very close to the original figure in the paper. Could you explain how do you set the 18 float numbers?  
> Thank you very much and best regards.
>  
> Yeping  
> > ------------------------------------------------------------------
> > From:Jared Sampson <jar...@co...>
> > Send Time:2018 Dec 6 (Thu) 12:09
> > To:孙业平 <sun...@al...>
> > Cc:pymol-users <pym...@li...>; "Smith, Paul" <pau...@kc...>
> > Subject:Re: [PyMOL] how to make selected residues blurry?
> >  
> > Hi Yeping -  
> >  
> > I had replied to your first email (on 11/30) with a similar suggestion to Paul's of using the `cartoon_transparency` setting, but now after looking at the original figure you're trying to replicate more closely, I realize that there isn't actually any transparency in that figure at all!  
> >  
> > The authors achieved this effect simply by using lighter and darker shades of ("palecyan" and "deepteal") for the hemagglutinin chain. The following script reproduces the original figure you shared almost exactly.  
> >  
> > bg_color white  
> > fetch 4gms, async=0
> >  
> >  
> > # hemagglutinin selections  
> > select ha, chain A
> >  
> > select l130, ha and resi 133-138
> >  
> > select l150, ha and resi 155-163
> >  
> > select h190, ha and resi 187-196
> >  
> > select l220, ha and resi 225-228
> >  
> > select loops, l130 or l150 or h190 or l220
> >  
> >  
> > # antibody selection  
> > select h2, chain H and resi 51-59
> >  
> > deselect
> >  
> >  
> > # basic view  
> > hide everything
> >  
> > as cartoon, ha
> >  
> > as cartoon, h2
> >  
> > cartoon tube
> >  
> >  
> > # colors  
> > color orange, h2
> >  
> > color palecyan, ha
> >  
> > color deepteal, loops
> >  
> >  
> > set_view (\  
> > -0.718157351, 0.514449000, -0.468602538,\
> >  
> > -0.667115033, -0.317360103, 0.673974276,\
> >  
> > 0.198008969, 0.796632588, 0.571111977,\
> >  
> > 0.000045628, -0.000060942, -75.169761658,\
> >  
> > 20.388980865, -23.567779541, 38.543788910,\
> >  
> > 52.026283264, 98.326217651, -20.000000000 )
> >  
> >  
> > set ray_opaque_background, 1  
> > ray 800, 800
> >  
> >  
> > I've uploaded the resulting image (with the script in the description) to PyMOL wiki: https://pymolwiki.org/index.php/File:4gms_colors.png  
> >  
> > Hope that helps.  
> >  
> > Cheers,  
> > Jared
> >  
> >  
> > On December 5, 2018 at 3:33:35 AM, sunyeping via PyMOL-users (pym...@li...(mailto:pym...@li...)) wrote:
> >  
> > Hi Paul,
> >  
> > Now I get closer to the final anwer!  
> > After following your steps, I get the effect I want. However, afer I "ray" the structure, a small part of the structure which I don't mean to set transparent become blur. Please see the image in the red circle in fig-3 (https://drive.google.com/file/d/1Au0LUkRKMCBCtN7XM_O0WlGKLhmtnyMV/view?usp=sharing).  
> > How does that happen and how to fix it?
> >  
> > Thank you again and best regards.  
> > Yeping
> > ------------------------------------------------------------------
> > From:Smith, Paul <pau...@kc...>
> > Send Time:2018 Dec 4 (Tue) 21:00
> > To:孙业平 <sun...@al...>; pymol-users <pym...@li...>
> > Subject:RE: [PyMOL] how to make selected residues blurry?
> >  
> >  
> > Hi Yeping,
> >  
> >  
> >  
> >  
> >  
> > To avoid this ‘breaking’ of your protein you will first need to create a copy of the entire molecule, set the transparency of the copy to your desired value, then hide the residues you want to make transparent on your original object.
> >  
> >  
> >  
> >  
> >  
> > So, you will do something like this:
> >  
> >  
> >  
> >  
> >  
> > # create a copy of your original object:
> >  
> >  
> > create new_obj, <original_object>
> >  
> >  
> >  
> >  
> >  
> > # set all residues on the copy to be transparent:
> >  
> >  
> > set cartoon_transparency, <value>, new_obj
> >  
> >  
> >  
> >  
> >  
> > # hide the residues you wish to be transparent on your original object:
> >  
> >  
> > select hide, <your_selection>
> >  
> >  
> > cartoon_skip, hide and <original_object>
> >  
> >  
> >  
> >  
> >  
> > This should prevent the your molecule from appearing to be broken.
> >  
> >  
> >  
> >  
> >  
> > Cheers,
> >  
> >  
> > Paul
> >  
> >  
> >  
> >  
> >  
> > From: sunyeping <sun...@al...>
> > Sent: Tuesday, December 4, 2018 3:23:00 AM
> > To: pymol-users; Smith, Paul
> > Subject: Re: [PyMOL] how to make selected residues blurry?  
> >  
> >  
> > Hi, Paul,
> >  
> > Thank you for your reply. I think the ‘set transparency’ command is on the correct direction, but there is another problem. In order to apply the ‘set transparency’, we should use "create" or "extract" command to make a new objective for the selected atoms. However, after I select the atoms that I want to make transparent, and use the command "extract":  
> > extract new_obj, sele
> > I find the new object is broken from the rest part of the structure. And then I use the commend:
> > set cartoon_transparency, 0.7, new_obj
> > The breaking between the new objective (the transparent part) and the rest part become more obvious. Please see the figure at the line (https://drive.google.com/file/d/1XQqGeN7JRLfSlexk4J7ufESWhnTJM3bW/view?usp=sharing).
> > Could you help me with the "breaking" problem?
> >  
> > Best regards,
> >  
> > Yeping
> >  
> >  
> >  
> > ------------------------------------------------------------------  
> > From:Smith, Paul <pau...@kc...>
> > Send Time:2018 Dec 3 (Mon) 20:38
> > To:孙业平 <sun...@al...>; pymol-users <pym...@li...>
> > Subject:RE: [PyMOL] how to make selected residues blurry?
> >  
> >  
> > Hi,
> >  
> >  
> >  
> >  
> >  
> > The ‘set transparency’ command will set the transparency of a surface (e.g. the interface between a protein and the surrounding water). I think the command you’re after is ‘set cartoon_transparency’ (https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels). Depending on your choice of representation, see also ‘set sphere_transparency’ and ‘set stick_transparency’.
> >  
> >  
> >  
> >  
> >  
> > Cheers,
> >  
> >  
> > Paul
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> > From: sunyeping via PyMOL-users(mailto:pym...@li...)
> > Sent: 03 December 2018 03:02
> > To: pymol-users(mailto:pym...@li...)
> > Subject: [PyMOL] how to make selected residues blurry?
> >  
> >  
> >  
> >  
> >  
> >  
> > Dear all,
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> > Could you please check this figure at the following link?
> >  
> >  
> >  
> > https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> > The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are: residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry.  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> > I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command:
> >  
> >  
> >  
> > set transparency, 0.8, sele
> >  
> >  
> >  
> > but it doesn't work.
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> > Could anyone help me figure it out？ With sincere thanks.
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> >  
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe  
>  

Re: [PyMOL] how to make selected residues blurry?

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

Hi Jared,

Your solution is very clever and helpful, but I don't know how to use the set_view command. I think it is vey important here because after this setting the scene becomes very close to the original figure in the paper. Could you explain how do you set the 18 float numbers? 
Thank you very much and best regards.

Yeping
 ------------------------------------------------------------------
From:Jared Sampson <jar...@co...>
Send Time:2018 Dec 6 (Thu) 12:09
To:孙业平 <sun...@al...>
Cc:pymol-users <pym...@li...>; "Smith, Paul" <pau...@kc...>
Subject:Re: [PyMOL] how to make selected residues blurry?


Hi Yeping  - 

I had replied to your first email (on 11/30) with a similar suggestion to Paul's of using the `cartoon_transparency` setting, but now after looking at the original figure you're trying to replicate more closely, I realize that there isn't actually any transparency in that figure at all!

The authors achieved this effect simply by using lighter and darker shades of ("palecyan" and "deepteal") for the hemagglutinin chain.  The following script reproduces the original figure you shared almost exactly.

bg_color white
fetch 4gms, async=0

# hemagglutinin selections
select ha, chain A
select l130, ha and resi 133-138
select l150, ha and resi 155-163
select h190, ha and resi 187-196
select l220, ha and resi 225-228
select loops, l130 or l150 or h190 or l220

# antibody selection
select h2, chain H and resi 51-59
deselect

# basic view
hide everything
as cartoon, ha
as cartoon, h2
cartoon tube

# colors
color orange, h2
color palecyan, ha
color deepteal, loops

set_view (\
    -0.718157351,    0.514449000,   -0.468602538,\
    -0.667115033,   -0.317360103,    0.673974276,\
     0.198008969,    0.796632588,    0.571111977,\
     0.000045628,   -0.000060942,  -75.169761658,\
    20.388980865,  -23.567779541,   38.543788910,\
    52.026283264,   98.326217651,  -20.000000000 )

set ray_opaque_background, 1
ray 800, 800

 I've uploaded the resulting image (with the script in the description) to PyMOL wiki: https://pymolwiki.org/index.php/File:4gms_colors.png

Hope that helps.

Cheers,
Jared

On December 5, 2018 at 3:33:35 AM, sunyeping via PyMOL-users (pym...@li...) wrote:
Hi Paul,

Now I get closer to the final anwer!
After following your steps, I get the effect I want. However, afer I "ray" the structure, a small part of the structure which I don't mean to set transparent become blur. Please see the image in the red circle in fig-3 (https://drive.google.com/file/d/1Au0LUkRKMCBCtN7XM_O0WlGKLhmtnyMV/view?usp=sharing). 
How does that happen and how to fix it? 

Thank you again and best regards.
Yeping
------------------------------------------------------------------
From:Smith, Paul <pau...@kc...>
Send Time:2018 Dec 4 (Tue) 21:00
To:孙业平 <sun...@al...>; pymol-users <pym...@li...>
Subject:RE: [PyMOL] how to make selected residues blurry?

Hi Yeping,
To avoid this ‘breaking’ of your protein you will first need to create a copy of the entire molecule, set the transparency of the copy to your desired value, then hide the residues you want to make transparent on your original object.
So, you will do something like this:
# create a copy of your original object:
create new_obj, <original_object>
# set all residues on the copy to be transparent:
set cartoon_transparency, <value>, new_obj
# hide the residues you wish to be transparent on your original object:
select hide, <your_selection>
cartoon_skip, hide and <original_object>
This should prevent the your molecule from appearing to be broken.
Cheers,
Paul

From: sunyeping <sun...@al...>
Sent: Tuesday, December 4, 2018 3:23:00 AM
To: pymol-users; Smith, Paul
Subject: Re: [PyMOL] how to make selected residues blurry?
Hi, Paul,

Thank you for your reply. I think the ‘set transparency’ command is on the correct direction, but there is another problem. In order to apply the ‘set transparency’, we should use  "create" or "extract" command to make a new objective for the selected atoms. However, after I select the atoms that I want to make transparent, and use the command "extract":
     extract new_obj, sele
I find the new object is broken from the rest part of the structure. And then I use the commend:
 set cartoon_transparency, 0.7, new_obj
The breaking between the new objective (the transparent part) and the rest part become more obvious. Please see the figure at the line (https://drive.google.com/file/d/1XQqGeN7JRLfSlexk4J7ufESWhnTJM3bW/view?usp=sharing).
    Could you help me with the "breaking" problem?
Best regards,
Yeping



------------------------------------------------------------------
From:Smith, Paul <pau...@kc...>
Send Time:2018 Dec 3 (Mon) 20:38
To:孙业平 <sun...@al...>; pymol-users <pym...@li...>
Subject:RE: [PyMOL] how to make selected residues blurry?

Hi,
The ‘set transparency’ command will set the transparency of a surface (e.g. the interface between a protein and the surrounding water). I think the command you’re after is ‘set cartoon_transparency’ (https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels). Depending on your choice of representation, see also ‘set sphere_transparency’ and ‘set stick_transparency’.
Cheers,
Paul
From: sunyeping via PyMOL-users
Sent: 03 December 2018 03:02
To: pymol-users
Subject: [PyMOL] how to make selected residues blurry?
Dear all,


Could you please check this figure at the following link?
https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing


The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are:  residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. 

I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command:
    set transparency, 0.8, sele
but it doesn't work.

Could anyone help me figure it out？ With sincere thanks.



_______________________________________________ 
PyMOL-users mailing list 
Archives: http://www.mail-archive.com/pym...@li...
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] how to make selected residues blurry?

[Jared S. <jar...@co...>]

Hi Yeping  - 

I had replied to your first email (on 11/30) with a similar suggestion to Paul's of using the `cartoon_transparency` setting, but now after looking at the original figure you're trying to replicate more closely, I realize that there isn't actually any transparency in that figure at all!

The authors achieved this effect simply by using lighter and darker shades of ("palecyan" and "deepteal") for the hemagglutinin chain.  The following script reproduces the original figure you shared almost exactly.

bg_color white
fetch 4gms, async=0

# hemagglutinin selections
select ha, chain A
select l130, ha and resi 133-138
select l150, ha and resi 155-163
select h190, ha and resi 187-196
select l220, ha and resi 225-228
select loops, l130 or l150 or h190 or l220

# antibody selection
select h2, chain H and resi 51-59
deselect

# basic view
hide everything
as cartoon, ha
as cartoon, h2
cartoon tube

# colors
color orange, h2
color palecyan, ha
color deepteal, loops

set_view (\
    -0.718157351,    0.514449000,   -0.468602538,\
    -0.667115033,   -0.317360103,    0.673974276,\
     0.198008969,    0.796632588,    0.571111977,\
     0.000045628,   -0.000060942,  -75.169761658,\
    20.388980865,  -23.567779541,   38.543788910,\
    52.026283264,   98.326217651,  -20.000000000 )

set ray_opaque_background, 1
ray 800, 800

I've uploaded the resulting image (with the script in the description) to PyMOL wiki: https://pymolwiki.org/index.php/File:4gms_colors.png

Hope that helps.

Cheers,
Jared

On December 5, 2018 at 3:33:35 AM, sunyeping via PyMOL-users (pym...@li...) wrote:

Hi Paul,

Now I get closer to the final anwer!
After following your steps, I get the effect I want. However, afer I "ray" the structure, a small part of the structure which I don't mean to set transparent become blur. Please see the image in the red circle in fig-3 (https://drive.google.com/file/d/1Au0LUkRKMCBCtN7XM_O0WlGKLhmtnyMV/view?usp=sharing). 
How does that happen and how to fix it?

Thank you again and best regards.
Yeping
------------------------------------------------------------------
From:Smith, Paul <pau...@kc...>
Send Time:2018 Dec 4 (Tue) 21:00
To:孙业平 <sun...@al...>; pymol-users <pym...@li...>
Subject:RE: [PyMOL] how to make selected residues blurry?

Hi Yeping,

 

To avoid this ‘breaking’ of your protein you will first need to create a copy of the entire molecule, set the transparency of the copy to your desired value, then hide the residues you want to make transparent on your original object.

 

So, you will do something like this:

 

# create a copy of your original object:

create new_obj, <original_object>

 

# set all residues on the copy to be transparent:

set cartoon_transparency, <value>, new_obj

 

# hide the residues you wish to be transparent on your original object:

select hide, <your_selection>

cartoon_skip, hide and <original_object>

 

This should prevent the your molecule from appearing to be broken.

 

Cheers,

Paul

 

From: sunyeping <sun...@al...>
Sent: Tuesday, December 4, 2018 3:23:00 AM
To: pymol-users; Smith, Paul
Subject: Re: [PyMOL] how to make selected residues blurry?
 
Hi, Paul,

Thank you for your reply. I think the ‘set transparency’ command is on the correct direction, but there is another problem. In order to apply the ‘set transparency’, we should use  "create" or "extract" command to make a new objective for the selected atoms. However, after I select the atoms that I want to make transparent, and use the command "extract":
     extract new_obj, sele
I find the new object is broken from the rest part of the structure. And then I use the commend:
     set cartoon_transparency, 0.7, new_obj
The breaking between the new objective (the transparent part) and the rest part become more obvious. Please see the figure at the line (https://drive.google.com/file/d/1XQqGeN7JRLfSlexk4J7ufESWhnTJM3bW/view?usp=sharing).
    Could you help me with the "breaking" problem?
Best regards,
Yeping



------------------------------------------------------------------
From:Smith, Paul <pau...@kc...>
Send Time:2018 Dec 3 (Mon) 20:38
To:孙业平 <sun...@al...>; pymol-users <pym...@li...>
Subject:RE: [PyMOL] how to make selected residues blurry?

Hi,

 

The ‘set transparency’ command will set the transparency of a surface (e.g. the interface between a protein and the surrounding water). I think the command you’re after is ‘set cartoon_transparency’ (https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels). Depending on your choice of representation, see also ‘set sphere_transparency’ and ‘set stick_transparency’.

 

Cheers,

Paul

 

 

From: sunyeping via PyMOL-users
Sent: 03 December 2018 03:02
To: pymol-users
Subject: [PyMOL] how to make selected residues blurry?

 

Dear all,




Could you please check this figure at the following link?

https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing




The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are:  residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. 

 

I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command:

    set transparency, 0.8, sele

but it doesn't work.

 

Could anyone help me figure it out？ With sincere thanks.

 

 

 

 



_______________________________________________  
PyMOL-users mailing list  
Archives: http://www.mail-archive.com/pym...@li...  
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] AttributeError: 'QFont' object has no attribute 'Monospace'

[Tran, Q. D <qd...@Ce...>]

Hello all,

Pymol svn 4190 could not find some font it was looking for. Pymol 1.9.0.0 ran fine without this problem.  How would I go about fixing this, maybe tell it to use another font?

Best,
Quyen

Re: [PyMOL] how to make selected residues blurry?

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

Hi Paul,

Now I get closer to the final anwer!
After following your steps, I get the effect I want. However, afer I "ray" the structure, a small part of the structure which I don't mean to set transparent become blur. Please see the image in the red circle in fig-3 (https://drive.google.com/file/d/1Au0LUkRKMCBCtN7XM_O0WlGKLhmtnyMV/view?usp=sharing). 
How does that happen and how to fix it? 

Thank you again and best regards.
Yeping
------------------------------------------------------------------
From:Smith, Paul <pau...@kc...>
Send Time:2018 Dec 4 (Tue) 21:00
To:孙业平 <sun...@al...>; pymol-users <pym...@li...>
Subject:RE: [PyMOL] how to make selected residues blurry?


Hi Yeping,
To avoid this ‘breaking’ of your protein you will first need to create a copy of the entire molecule, set the transparency of the copy to your desired value, then hide the residues you want to make transparent on your original object.
So, you will do something like this:
# create a copy of your original object:
create new_obj, <original_object>
# set all residues on the copy to be transparent:
set cartoon_transparency, <value>, new_obj
# hide the residues you wish to be transparent on your original object:
select hide, <your_selection>
cartoon_skip, hide and <original_object>
This should prevent the your molecule from appearing to be broken.
Cheers,
Paul

From: sunyeping <sun...@al...>
Sent: Tuesday, December 4, 2018 3:23:00 AM
To: pymol-users; Smith, Paul
Subject: Re: [PyMOL] how to make selected residues blurry?
Hi, Paul,

Thank you for your reply. I think the ‘set transparency’ command is on the correct direction, but there is another problem. In order to apply the ‘set transparency’, we should use  "create" or "extract" command to make a new objective for the selected atoms. However, after I select the atoms that I want to make transparent, and use the command "extract":
     extract new_obj, sele
I find the new object is broken from the rest part of the structure. And then I use the commend:
 set cartoon_transparency, 0.7, new_obj
The breaking between the new objective (the transparent part) and the rest part become more obvious. Please see the figure at the line (https://drive.google.com/file/d/1XQqGeN7JRLfSlexk4J7ufESWhnTJM3bW/view?usp=sharing).
    Could you help me with the "breaking" problem?
Best regards,
Yeping



------------------------------------------------------------------
From:Smith, Paul <pau...@kc...>
Send Time:2018 Dec 3 (Mon) 20:38
To:孙业平 <sun...@al...>; pymol-users <pym...@li...>
Subject:RE: [PyMOL] how to make selected residues blurry?


Hi,
The ‘set transparency’ command will set the transparency of a surface (e.g. the interface between a protein and the surrounding water). I think the command you’re after is ‘set cartoon_transparency’ (https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels). Depending on your choice of representation, see also ‘set sphere_transparency’ and ‘set stick_transparency’.
Cheers,
Paul
From: sunyeping via PyMOL-users
Sent: 03 December 2018 03:02
To: pymol-users
Subject: [PyMOL] how to make selected residues blurry?
Dear all,


Could you please check this figure at the following link?
https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing


The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are:  residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. 

I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command:
    set transparency, 0.8, sele
but it doesn't work.

Could anyone help me figure it out？ With sincere thanks.

[PyMOL] Help_regarding_Transformation_matrix

[Fedaa N. <fed...@ya...>]

Hello,  After optimizing the Iron-sulfur clusters existing in the photosystem I, the coordinates transforms to another frame, what I need to do is to transfer back to the original coordinates by getting the transformation matrix.

here what I did ..using pymola1- I loaded post and pre-processing object2- I aligned them together3- I tried to get the transformation matrix with this commandprint cmd.get_object_matrix("pre-processing object")and this step returns a 4*4 matrices (-0.017042629420757294, 0.6273888349533081, -0.7785196304321289, -27.565351122804373, 0.15071848034858704, 0.7713475823402405, 0.6183096766471863, -142.13367787636093, 0.9884297847747803, -0.1067996621131897, -0.10770488530397415, -81.02178268868633, 0.0, 0.0, 0.0, 1.0)finally,  I used this command to apply the matrix ...cmd.transform_object( "post_processing object", [-0.017042625695466995, 0.15071852505207062, 0.9884297847747803, 101.03673254990264, 0.6273888349533081, 0.7713475823402405, -0.10679969936609268, 118.27556096672724, -0.7785196304321289, 0.6183096766471863, -0.10770490765571594, 57.69601938212094, 0.0, 0.0, 0.0, 1.0])am I doing it in a correct way ??and I need to find the transformed structure, how I could do it ?
Thank you,  Fedaa Ali 

Re: [PyMOL] how to make selected residues blurry?

[Smith, P. <pau...@kc...>]

Hi Yeping,

To avoid this ‘breaking’ of your protein you will first need to create a copy of the entire molecule, set the transparency of the copy to your desired value, then hide the residues you want to make transparent on your original object.

So, you will do something like this:

# create a copy of your original object:
create new_obj, <original_object>

# set all residues on the copy to be transparent:
set cartoon_transparency, <value>, new_obj

# hide the residues you wish to be transparent on your original object:
select hide, <your_selection>
cartoon_skip, hide and <original_object>

This should prevent the your molecule from appearing to be broken.

Cheers,
Paul

________________________________
From: sunyeping <sun...@al...>
Sent: Tuesday, December 4, 2018 3:23:00 AM
To: pymol-users; Smith, Paul
Subject: Re: [PyMOL] how to make selected residues blurry?

Hi, Paul,

Thank you for your reply. I think the ‘set transparency’ command is on the correct direction, but there is another problem. In order to apply the ‘set transparency’, we should use  "create" or "extract" command to make a new objective for the selected atoms. However, after I select the atoms that I want to make transparent, and use the command "extract":
     extract new_obj, sele
I find the new object is broken from the rest part of the structure. And then I use the commend:
     set cartoon_transparency, 0.7, new_obj
The breaking between the new objective (the transparent part) and the rest part become more obvious. Please see the figure at the line (https://drive.google.com/file/d/1XQqGeN7JRLfSlexk4J7ufESWhnTJM3bW/view?usp=sharing).
    Could you help me with the "breaking" problem?

Best regards,

Yeping



------------------------------------------------------------------
From:Smith, Paul <pau...@kc...>
Send Time:2018 Dec 3 (Mon) 20:38
To:孙业平 <sun...@al...>; pymol-users <pym...@li...>
Subject:RE: [PyMOL] how to make selected residues blurry?

Hi,

The ‘set transparency’ command will set the transparency of a surface (e.g. the interface between a protein and the surrounding water). I think the command you’re after is ‘set cartoon_transparency’ (https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpymolwiki.org%2Findex.php%2FCartoon%23Various_Transparency_Levels&data=01%7C01%7Cpaul.smith%40kcl.ac.uk%7Ccf93cb90e1834838588a08d65997dd36%7C8370cf1416f34c16b83c724071654356%7C0&sdata=h82rBhFhb%2FU7sha1Gt5FGpOe%2BZ0oAJ8tA7KxC4Zl%2FT8%3D&reserved=0>). Depending on your choice of representation, see also ‘set sphere_transparency’ and ‘set stick_transparency’.

Cheers,
Paul


From: sunyeping via PyMOL-users<mailto:pym...@li...>
Sent: 03 December 2018 03:02
To: pymol-users<mailto:pym...@li...>
Subject: [PyMOL] how to make selected residues blurry?

Dear all,


Could you please check this figure at the following link?
https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0%2Fview%3Fusp%3Dsharing&data=01%7C01%7Cpaul.smith%40kcl.ac.uk%7Ccf93cb90e1834838588a08d65997dd36%7C8370cf1416f34c16b83c724071654356%7C0&sdata=4g1hw5KnhhRjRDo0d2DVc1hSrJJTSbmwlCgsGFP1Lw0%3D&reserved=0>


The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are:  residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry.

I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command:
    set transparency, 0.8, sele
but it doesn't work.

Could anyone help me figure it out？ With sincere thanks.