Re: [PyMOL] Question Regarding Timeline Python API Availability in Open-Source PyMOL

e. Are there any plans for it > to be open source one day? > > Best regards, > Martin > On 20.01.2025 19:44, Jarrett Johnson wrote: > > Hi Martin, > > Timeline and its corresponding Python API is only available for on > Incentive versions. > > Jarrett J.

Re: [PyMOL] Question Regarding Timeline Python API Availability in Open-Source PyMOL

nce. > > Best regards, > Martin > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarre

Re: [PyMOL] About license question

ps://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.n

Re: [PyMOL] Create command with ranges of states

__ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL __

Re: [PyMOL] Pymol 3 Timeline issues

>> ___ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > ___ > PyMOL-users mailing lis

Re: [PyMOL] Pymol 3 Timeline issues

gt; Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http

Re: [PyMOL] BCIF

_ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL ___

Re: [PyMOL] `set grid_mode, 1` not working on a pml script?

hing. > > > El lun, 20 may 2024 a la(s) 12:36 p.m., Jarrett Johnson ( > jarrett.john...@schrodinger.com) escribió: > >> Hi Francisco, >> >> Which version of PyMOL are you using? >> >> Jarrett J. >> >> On Mon, May 20, 2024 at 2:30 PM Franc

Re: [PyMOL] `set grid_mode, 1` not working on a pml script?

_ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL __

Re: [PyMOL] Exporting movie as PNG frames produces only single frame

> PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] Announcing PyMOL 3.0 Release

Cheers, - The PyMOL Team at Schrödinger -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol

Re: [PyMOL] labels on nucleic acids

__ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > -- *Jarrett Johnson* | Senior Developer, PyMOL __

Re: [PyMOL] create new object from selection - version 3.0

6Sp2TTu?domain=mackaymatthewslab.org> > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe >

Re: [PyMOL] Pymol Getting rid of the Colorbar

nd it worked. Many thanks! > Best regards, > > Anna > On 29.11.2023 04:47, Jarrett Johnson wrote: > > Hi Anna, > > Toggling an object's activity by clicking on the GUI uses the underlying > *disable > *command. If you already know the name of the color ramp, you

Re: [PyMOL] Pymol Getting rid of the Colorbar

__ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL _

Re: [PyMOL] Vacuum Electrostatics error

-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Map to cartoon

rrett J On Mon, Jul 24, 2023 at 1:27 PM Foster, Mark wrote: > Thanks Jarrett for the response. > > > > I think `spectrum` should work, but I can’t figure out how to access the > proximity parameter calculated by `ramp_new` in order to use it directly > (e.g., “p.prox”), or t

Re: [PyMOL] Map to cartoon

resiliency of these tribal nations and > recognize the historical context that has and continues to affect the > Indigenous peoples of this land. > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-u

Re: [PyMOL] Question on residue selection in multiple PDB

Sorry, typo. For the second approach, state should be `i + 1` and not `-1`" Jarrett J. On Thu, Jul 20, 2023 at 8:49 AM Jarrett Johnson < jarrett.john...@schrodinger.com> wrote: > Hi Neena, > > Is the split_states necessary? You can query the distance between atoms on >

Re: [PyMOL] Question on residue selection in multiple PDB

> structures and find polar contacts within this selection? >> >> Many thanks, >> Neena >> > ___________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe:

Re: [PyMOL] Distance measure between pseudo atoms does not update over states

list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL ''' See more here: http://www.pymolwiki.org/index.php/cen

Re: [PyMOL] Help with selecting interface residues between two structures

ponding residues in object “pred”? > > > > In addition, what if in the pred structure, chains are named A, B, and C, > corresponding to base structure L, H, A, respectively, how will I handle > that? > > (I was planning to rename the chains, if there is no nice trick to > t

Re: [PyMOL] Edu-PyMOL for master thesis

gt; Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mai

Re: [PyMOL] reset TTT matrix to identity

ng the matrix values with the object kept in its new > position. > Regards, > Philip > > On Fri, Jun 2, 2023 at 12:56 PM Jarrett Johnson < > jarrett.john...@schrodinger.com> wrote: > >> Hi Philip, >> >> Have you tried the `matrix_reset` command instead?

Re: [PyMOL] reset TTT matrix to identity

an provide. > Regards, > Philip > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Generating of Rg for every state in PyMOL

; Jessica Lim > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > -- *Jarrett Johnson* | S

Re: [PyMOL] Surface and cartoon transparency together?

sts/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] PLEASE HELP

d really appreciate it. I'm > really stuck and in need of help. > > Thanks so much in advance, > > Kyle > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net &g

Re: [PyMOL] Loading gromacs and amber trajectory

cts/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Solid stick between two residues?

rs@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] pymol for educational purpose

_ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL ___

Re: [PyMOL] invalid namespace

Can anyone help? Thanks. > > -- > Criss Hartzell > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/py

[PyMOL] PyMOL Announcements (Fellowship & Future of PyMOL)

PyMOL. Stay tuned for more details on our website about PyMOL 3.0 and our future roadmap later this year. Best, PyMOL Development Team -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol

Re: [PyMOL] Question about glm in pymol

Hi, Your version of glm (default with Centos7 with yum) should now work. I committed a change to fix this compiler error about twelve hours ago. You just need to pull the latest changes. Best, Jarrett J. On Tue, Jul 12, 2022 at 10:24 PM 张敏华 wrote: > Dear Jarrett Johnson： > In

Re: [PyMOL] Question about glm in pymol

ling list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list A

Re: [PyMOL] Did not recieve Email

w.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mail-archive

Re: [PyMOL] "PyMOL-users" mailing list

ve questions about PyMOL. > > Kind regards, > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubsc

Re: [PyMOL] EduPymol Not sending Liscene

e: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: http

Re: [PyMOL] pymol education license

_ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL _

Re: [PyMOL] pair_fit crashes Pymol 2.5.2 (incentive, OSX) ?

Hi James, This is a known issue. Try disabling undo before using the command. Best, Jarrett Johnson On Mon, Feb 14, 2022 at 10:37 AM James Procter (Staff) < j.proc...@dundee.ac.uk> wrote: > Dear pymol-users > > Could anyone confirm that the following test of the pair_fit com

Re: [PyMOL] PyMOL for M1 macs

on via Conda install? > See here: https://pymol.org/2/support.html? > Supported platform states M1 with rosetta2. Perhaps with some penalty for > efficiency though. Anyone tried? > > Sent from my iPhone > > On Dec 5, 2021, at 10:27 PM, Jarrett Johnson < > jarrett.john...@s

Re: [PyMOL] PyMOL for M1 macs

uild of PyMOL for M1 Macs yet? > > Cheers, > > Chris > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pym

Re: [PyMOL] About contacting the PYMOL-creators

Regards, > K. Zeghida. > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer [image: Schr

Re: [PyMOL] help - password cracked

dvice as to how to solve this. > > Many thanks in advance! > > Best, > > Joli > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projec

Re: [PyMOL] Labeling residues for publication

> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer [image: Schrodinger Logo] <https://www.schrodinger.com/> ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@

Re: [PyMOL] Labeling residues for publication

> > On 28.10.2021, at 14:40, Jarrett Johnson > wrote: > > Hi George, > > This issue should've been addressed in PyMOL 2.5.1. I would consider > upgrading if you can. > > Best, > Jarrett J > > On Thu, Oct 28, 2021 at 9:31 AM George Tzotzos via PyMOL-user

Re: [PyMOL] AxPyMOL

problem? > > > > Thank you all very much. > > > > Michael > > > > > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe:

Re: [PyMOL] pymol installation error

ubstitution failed: > > layer1/Scene.cpp:2557:42: note: mismatched types ‘const T*’ and > ‘glm::tvec3’ > > I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ > ^ > error: command 'g++' failed with exit sta

Re: [PyMOL] Custom zoom settings

tp://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer [image: Schrodinger Logo] <https://www.schrodinger.com/> ___

Re: [PyMOL] small GUI font size

___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer [image: Schrodinger Logo] &

[PyMOL] PyMOL 2.5.1 Released

classroom and connect you with educators from all over the world. https://www.schrodinger.com/conferences-meetings/2021-schrodinger-educators-day-online As always, we welcome any feedback and bug reports. Cheers, - The PyMOL Team at Schrödinger -- *Jarrett Johnson* | Senior Developer [image

Re: [PyMOL] PyMOL 2.5 released

m/schrodinger/pymol-open-source.git? > > On 05/10/2021 12:27 PM, Jarrett Johnson wrote: > > Greetings, > > We are happy to announce the release of PyMOL 2.5. Download ready-to-use > bundles from https://pymol.org/ or update your installation with "conda > install

[PyMOL] PyMOL 2.5 released

converter tools including 2to3 may be useful if you need to update python scripts. Find the complete release notes at: https://pymol.org/d/media:new25 We welcome any feedback and bug reports. Cheers, - The PyMOL Team at Schrödinger -- *Jarrett Johnson* | Senior Developer [image: Schrodinger Lo

Re: [PyMOL] Cartoon_transparency

> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer [image: Schrodinger Logo] <https://www.schrodinger.com/> ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@l

Re: [PyMOL] Pymol in conda-forge osx-arm64 for new M1 Macs

subscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer [image: Schrodinger Logo] <https://www.schrodinger.com/> ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/py

Re: [PyMOL] Custom selection operators

et > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > -- *Jarrett Johnson* | Senior Developer [image: Schrodinger Logo] <https://www.schrodinger.com/> ___ PyMOL-users mailing list Archives: http://w

Re: [PyMOL] renumber

scribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer [image: Schrodinger Logo] <https://www.schrodinger.com/> ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users

Re: [PyMOL] Extract all phi and psi angles

thanks, > Neena > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior D

Re: [PyMOL] Can't install latest version on Mac

ory > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > United Kingdom > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforg

Re: [PyMOL] Open source v2.3.3

Campus > Hinxton > Cambridge CB10 1SD > United Kingdom > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscr

Re: [PyMOL] Ray tracing transparent sticks

much. > > All the best, > Yannis > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsu

Re: [PyMOL] Problem with PDB file export

Shein-Lumbroso* > *m:* +61 406 276 801 | *e: *ofir.sh...@gmail.com > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/un

Re: [PyMOL] Space group Symmetry operators

Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Jarrett Johnson PyMOL Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubsc

Re: [PyMOL] Open source PyMOL 2.4

researcher in Yokohama, Japan > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe >

Re: [PyMOL] PyMOL 2.3 released

TBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=WVkM4La4mZsWQ2beQpPA_hXCmu_AFvn6RbGtetuCDqA&e= > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://

Re: [PyMOL] Artificial Lines for Sticks

ves: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Jarrett Johnson PyMOL Developer Schrödinger, Inc. ___ PyMOL-users mailing list

Re: [PyMOL] distance

nux_Install > > > Cheers, > > Joseph. > > > > Joseph S. Brock | PhD > Researcher > Drew Lab > Department of Biochemistry and Biophysics > Stockholm University > -- > *From:* Jarrett Johnson > *Sent:* Thursday, 25 October 2018 11:34:

Re: [PyMOL] distance

t; > Joseph S. Brock | PhD > Researcher > Drew Lab > Department of Biochemistry and Biophysics > Stockholm University > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > U

Re: [PyMOL] Mojave support

pplication. On Fri, Sep 28, 2018 at 2:14 PM Jack Vizelter wrote: > Is Mojave then officially supported with PyMol? > > > > > > > > *From: *Jarrett Johnson > *Date: *Friday, September 28, 2018 at 12:59 PM > *To: *"sa...@umich.edu" > *Cc: *Pymol User

Re: [PyMOL] Mojave support

> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jarrett Johnson PyMOL Developer Schrödinger, Inc. ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinf

Re: [PyMOL] Graphics display not working

sites, Slashdot.org! http://sdm.link/slashdot > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: ht

Re: [PyMOL] Add to existing selection

e: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jarrett Johnson, Schrödinger

Re: [PyMOL] Preventing Output of pair_fit

Hello Nathan, While we prepare to rollout the "quiet" argument for pair_fit, in the meantime try: cmd.feedback("disable", "executive", "results") Jarrett J. On Sun, Jul 22, 2018 at 6:47 PM, Jarrett Johnson < jarrett.john...@schrodinger.com>