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; # save output as pdb
> # I need to add something in the name of output indicating how much
> chains have been renamed
> # like output_withoutAB.pdb
> cmd.save('output_' + '.pdb')
>
> thanks in advance for help!
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
___
>
> Thanks in advance!
>
> вт, 25 июн. 2019 г. в 14:50, James Starlight :
>>
>> I have got the idea!
>> thank you so much Thomas!
>> One question: generally if I integrate a pymol silent script inside my
>> bash script, I do not need to use cmd.* s
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Hi Arnaud,
This should be fixed now, see
https://github.com/schrodinger/pymol-open-source/commit/af28e453c6
Cheers,
Thomas
> On Jun 13, 2019, at 5:46 PM, Thomas Holder
> wrote:
>
> Hi Arnaud,
>
> I can reproduce both issues, at least with "sticks" represe
of Biochemistry Tel: ++44 (0)1865 (2)75392
> University of Oxford
> Oxford UK, OX1 3QU
>
>
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X-ray facilities manager
> Newcastle Structural Biology Laboratory
> University of Newcastle
> Medical School
> ICAMB
> Framlington place
> NE2 4HH Newcastle upon tyne
> Phone 0191 208 8931
>
>
>
> ___
> PyMOL
le or approach? Any advice or suggestions will
> be greatly appreciated.
>
> Kind regards,
>
> Taka
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> ht
t pymol
> from updating the rendering between each cmd.bond call?) or at least an API
> function that better exposes the bond generation procedure. Does someone have
> suggestions on how to solve this problem?
>
> Cheers,
> Lorenzo
>
..
>
> Thanks for any hints.
>
> Best,
>
> Jan
>
> --
> Dr. Jan Gebauer
> AG Prof. Baumann
> Institut für Biochemie / Uni-Köln
> Zülpicher Str. 47 / 50674 Köln
> Fon: +49 (221) 470 3212
> Fax: +49 (221) 470 5066
>
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Schrödin
h part become blur? Is there better way to make the ligand blur?
>
> Thank you very much!
>
> Arthur
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> Sincerely,
> JuK
>
>
> P.S. If i broke any rule of support-requesting or if any information is
> missing please let me know.___
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Dept. of Biology, Purdue University
> PULSe-Biophysics and Structural Biology training group
> vpur...@purdue.edu | 346-719-9409
>
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gt;
>> ___
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>
> _
regards,
>
> Ali Kusay
> PhD student
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> up pymol on my computer that would be greatly appreciated.
>
> Thank you,
>
> Julia Garcia
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_begin,ref_end) )
>
>## here I loop over all residues in the sliding window and calculte the
> rmsd for my residues of interest.
> for g in calpha.atom : I loop over the slinding window
> if g.resi == str(j[0]): ## we select only our residue of interest
> within the
e cmd.get_model in my version.
> but there is document of 'get_model' in pymol wiki
> (https://pymolwiki.org/index.php/Get_Model)
> is it replaced some other cmd?
> I want to use 'cmd.get_model', if anyone can give the python code of
> 'get_model'?
>
> Thanks
>
>
ical Institute
>>>> Stanford University School of Medicine
>>>> Beckman B177, 279 Campus Drive, Stanford CA 94305
>>>> Phone: (650) 723-6431
>>>>
>>>> On Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg
>>>> wrote:
>>>&
parsing.py", line 532, in
> run_file
>execfile(file,global_ns,local_ns)
> File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 526, in
> execfile
>co = compile(pi.file_read(filename), filename, 'exec')
> File "/home/mheller
lrc.pml file. However, it seems it creates a new
> file. All operations from last time are wiped out.
>
> “Append…” from “File -> Log File” menu seems work. But how can I make it
> automatically for every time pymol is open? It seems there is no “log_append”
> command.
&g
has experience in this aspect, please feel free to advise.
>
> Many thanks.
>
> William
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licfile = get_license_filename_user()
> File "C:\ProgramData\PyMOL\lib\site-packages\pymol\licensing.py", line 75,
> in get_license_filename_user
> filename = os.path.expanduser(filename)
> File "C:\ProgramData\PyMOL\lib\ntpath.py", line 311, in expa
hose in presets and so on.
>
> There is some verbose option that does it?
>
> Thank you,
> Pedro Lacerda
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Prague, Czech Republic
> &
> CEITEC - Central European Institute of Technology
> Brno, Czech Republic
>
> email: teva...@gmail.com
> website: https://sites.google.com/site/thomasevangelidishomepage/
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
> Dr Thomas Evangelidis
> Research Scientist
> IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
> of Sciences
> Prague, Czech Republic
> &
> CEITEC - Central European Institute of Technology
> Brno, Czech Republic
>
> email: teva...@
Hi all,
If you have Python scripts or plugins which aren't Python 3 compatible yet, you
might find this guide useful:
https://pymolwiki.org/index.php/2to3
Cheers,
Thomas
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
___
PyMOL
7/site-packages/pymol/_cmd.so:
> undefined symbol: MMTF_unpack_from_string
>
> Any idea what is going wrong?
>
> Thank you for your help.
>
> Best
> Heng-Keat
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
__
18.2.2
>> Traceback (most recent call last):
>> File
>> "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/__init__.py",
>> line 27, in run
>> from .PMGApp import PMGApp
>> File
>> &q
ymol/_cmd.cpython-36m-x86_64-linux-gnu.so:
> undefined symbol: glutSwapBuffers
>
> Cheers
>
> Tru
> --
> Dr Tru Huynh | mailto:t...@pasteur.fr | tel +33 1 45 68 87 37
> https://research.pasteur.fr/en/team/structural-bioinformatics/
> Institut Pasteur, 25-28
{PYTHON_V}
> python3 setup.py build
> python3 setup.py install --prefix=/
>
> for python2, I just resplaced python3 by python in the lines above.
>
> Any idea what could be causing this behaviour?
>
> Cheers
>
> Tru
>
> --
> Dr Tru Huynh | mailto:t...@past
Sent: Monday, February 11, 2019 7:20 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] dark structure
>
> Hi,
>
> Is there any one who knows why the structure look so dark in pymol (see
> attached)? I have tried re-install the software but doesn’t work.
>
e:
>
>
> Hi,
>
> I am using pymol with a wxpython interface and everything seems to work,
> except when I try to change the color of an object using the internal gui, I
> get a NameError: name 'util' is not defined error... can you see what is the
> problem here?
&g
am.
>
> 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
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
___
PyMOL-users ma
elcome any feedback and bug reports.
Cheers,
- The PyMOL Team at Schrödinger
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Unsubscri
> 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.
_
kages/pandas/__init__.py", line
> 51, in
> plot_params = pandas.plotting._style._Options(deprecated=True)
>
> I'd really appreciate your help with this!
> Kind regards,
> Andreas
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
__
rather strange and very inconvenient for work.
> Problem appears only at 1920x1080 resolution and everything is fine at lower
> resolution. I have uploaded screenshots from pymol 2 at 1920x1080 (highDPI)
> and 1680x1050 (lowDPI) here:
> https://imgur.com/a/Tlp79Kq
>
> Do anyone have
that s/he can continue to develop free resources to
help scientific progress and the community as a whole. You can read more about
the PyMOL Open Source Fellowship Program and the fellows at
https://pymol.org/fellowship
Cheers,
The PyMOL Team at Schrödinger
--
Thomas Holder
PyMOL Principal
Hi Sophia,
Regarding X forwarding on macOS: It turns out iglx is disabled by default since
XQuartz 2.7.10. After enabling it, PyMOL works. I've put this information on
the PyMOLWiki:
https://pymolwiki.org/index.php/Remote_Desktop
Cheers,
Thomas
> On Nov 19, 2018, at 1:36 PM, Thomas Hol
white, no matter what I try to load.
>
> How can I get the bottom display to work ?
>
> Thank you,
> Sophia
>
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PyMOL Principal Developer
Schrödinger, Inc.
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Archives: http://www.mail-
mmand separately works as expected. The error message shows up
> only if "label *, name" is followed by another command, on the same line.
>
> I am using "Version 1.8.7.0 Open-Source" on macOS.
>
> Any ideas?
>
> Thanks,
>
> Xi
Hi Yufeng,
This is a problem with a recent graphics driver update from Intel on
Windows 10. So far it appears that the build series "4.5.0 - Build
24.20.100." is affected. Can you please tell us what PyMOL reports
as "OpenGL graphics engine" (3 lines printed in log window on
startup)?
Hi Steve and Shintaro,
Shintaro is right, PyMOL's ray tracing is CPU only. It runs parallel
on multiple CPU cores.
Our graphics development over the last years was focused on getting
the real-time OpenGL rendering (which uses the GPU heavily) as close
to the ray traced images as possible.
, an object is created but no dashed lines appear. When I "zoom"
> this object it is very far in space from the atoms I selected to make the
> distances between, and there is still nothing I can do to make the dashed
> lines appear.
>
> If anyon
the PyQt thread
to support old plugins.
Cheers,
Thomas
> On Oct 16, 2018, at 6:59 PM, David Mathog wrote:
>
> On 16-Oct-2018 00:07, Thomas Holder wrote:
>>> On Oct 15, 2018, at 9:38 PM, David Mathog wrote:
>>> There must be something about Qt that is a significant i
s you expect, you should file a
bug report with Ubuntu.
Cheers,
Thomas
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t (we've seen unusable graphics on Intel/Windows)
- viewport size issues with multiple screens on Windows
On top of that, we get:
- trackpad support (pinch zoom)
- file open with drag-n-drop
Cheers,
Thomas
--
Thomas Holder
PyMOL Principal Deve
ens two windows -
> unlike Pymol on macos.
>
> Does anyone knows how to make it run in one window?
>
> Thanks,
>
> Itamar
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PyMOL Principal Developer
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How it
> can be done. Please help.
> Thanking you
> Regards
> Abhik
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p1.startWithTclTk()
> File "/.../anaconda3/lib/python3.6/site-
> packages/pymol2/__init__.py", line 145, in startWithTclTk
> sys.modules[gui].__init__(self,poll,skin)
> TypeError: module.__init__() takes at most 2 arguments (3
> given)
>
>
>
&g
If you need to be unsubscribed from this list, please email me directly and I
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Or, you can visit this page and unsubscribe yourself:
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Thanks,
Thomas
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PyMOL Principal Developer
Schrödinger
similar
> problems and had a solution. I have tried uninstalling and reinstalling from
> both exe installer and zip archive. Neither have fixed the problem. Thanks
> for your help.
>
> Ryan Kung
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
__
instructions on how to install PyMOL on CentOS 7
> Thanks
> --
> Puneet
--
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> represent heavy atoms?
>
> What are the differences between backbone and heavy atoms? How to compute
> pairwise RMSD for a lot of structures? Can I use align here?
>
> Thank you very much.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
---
> On Aug 22, 2018, at 4:55 PM, abhik.gh...@bose.res.in wrote:
>
> Hello All
> I want to know how the "Extra_fit" option works in pymol (Detail algorithm
> or procedure). Any idea regarding this.
> All suggestions are welcome.
> Thank you.
--
Thomas Holder
PyMOL
Zn2+ or Mg2+,
> that doesn't require manual selection of atoms and showing of bonds?
>
> I wasn't able to find anything online ...
>
> Thanks
> Markus
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
cube file. ( .cube is an extension). These cube files are from
> Delphi. ( Poisson Boltzmann solver).
>
> Thank you ,
>
> Best Regards
> Divya
>
> Get Outlook for iOS
> From: Thomas Holder
> Sent: Friday, August 17, 2018 4:51 AM
> To: Divya Kaur Matta
> Cc: pymol-us
yMol 2.0, but only a phosphorous can be added to the serine. Does
> anyone have experiences of creating a phosphorylated residue with PyMol or
> other tools?
> Any suggestions would be appreciated.
>
> Thanks,
> Wei
--
Thomas Holder
PyMOL Principal Developer
Schrödinge
p20
>
> For slice,
>
> I did actions, show slice(default)
>
> Please find attached images for the slice I got.
>
>
> Thank you!
>
> Best Regards,
>
> Divya K. Matta
> Ph.D. Student in Chemistry
--
Thomas Holder
PyMOL Principal Developer
Schröd
; w.r.t "avg.pdb" file. I can do it manually using align command i.e align
> 1, avg. But is there any code or anything by which i can produce alignment
> files and save them as new pdb.
> Any suggestion is welcome
> Thank you
> Abhik
--
y 30, 2018 at 2:16:54 AM, abhik.gh...@bose.res.in
> (abhik.gh...@bose.res.in) wrote:
>
>> Hello All
>> I have a pdb file containing 10 frames . Now I want to align all frame
>> one by one in pymol and then want to save the final coordinate. How it can
&g
;>>
>>>> It works but I obtained an abnormal high RMSD value of 6.146 A. When I use
>>>> the
>>>> pair_fit function, pymol completely return one molecule and also write
>>>> "ExecutiveRMS: RMS =6.146 (51 to 51 atoms)". I should have
d_crystal*, /ligand_docking*
>>>
>>> It works but I obtained an abnormal high RMSD value of 6.146 A. When I use
>>> the
>>> pair_fit function, pymol completely return one molecule and also write
>>> "ExecutiveRMS: RMS =6.146 (51 to 51 atoms
te any suggestions and ideas.
>
> Best,
> Wei
>
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PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant tech community on one of the world's most
engaging
layman’s terms and
> stepwise approach it would be very helpful.
>
> Any help is much appreciated.
>
> Thank you!
--
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PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant t
ib/x86_64-linux-gnu/qt5/plugins/xcbglintegrations/libqxcb-egl-integration.so
> /usr/lib/x86_64-linux-gnu/qt5/plugins/xcbglintegrations/libqxcb-glx-integration.so
>
>
> Any idea how to solve this issue?
>
> Thanks.
> M.
--
Thomas Holder
PyMOL Principal Developer
Schrödinge
ion "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_
it possible to force align to give the full RMSD calculation? super has
> the same issue, and I'm concerned that using something like rms or fit won't
> work because the "gold" and "test" have different residue numbering (and
> might be missing residues so it's not always
t; Biotechnology Dept.
> IIT Madras
> Chennai-600036
>
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PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant tech community on one of the world's mos
the pymol-users mailing list provided by SourceForge.
Cheers,
Thomas
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--
Check out the vibrant tech community on one of the world's most
engaging tech sites
ot look truncated
> sele = 'sc. and i. or name ca and i. {}'.format(stored.x)
> This works but it centers on the ca and not the sc. Plus... sticks are not
> drawn.
> Ps. Sorry for the delay. I was very sick.
>
>
>
> 2018-06-18 5:12 GMT-05:00 Thomas Holder :
>
&g
sele = 'sc. and i. {}'.format(stored.x)
Cheers,
Thomas
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slash
a quick look at how well my electron density fits
> to all my models...
>
> Thanks
>
> ------
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
-
to develop free resources to help
scientific progress and the community as a whole.
Details and application instructions can be found on
https://pymol.org/fellowship
The application deadline is August 26, 2018.
We look forward to your submissions!
Cheers,
The PyMOL Team at Schrödinger
--
Thomas
o/modules/ADT/mglutil/util/misc.py",
>> line 19, in
>> import numpy.oldnumeric as Numeric
>> ImportError: No module named oldnumeric
>>
>> Hope someone can help me or point me in the right direction.
>>
>> Best regards,
>> E
Hi Gianluca,
> is it possible to set ambient occlusion for isosurfaces?
Unfortunately no, it's only implemented for molecular surfaces.
Cheers,
Thomas
--
Thomas Holder
PyMOL Principal Developer
Schrödinger,
t; from the element (which I imagine must be possible, but I haven't
> found a clear example of how to do this), that would be the most preferred
> option, as it would allow us to use a single sphere element per
> output file.
>
> Thanks to Gary for bringing this up.
or is it still OpenGL based?
>
> Thanks,
>
> David Mathog
> mat...@caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
-
r and export/import faster,
> I think, if it used geometry_instance for spheres rather than giving each
> sphere its own geometry/mesh/accessors/etc.. Has that been discussed before?
>
> --
> Gary Oberbrunner
--
Thomas Holder
PyMOL Principal
?
>
> System is linux Mint 18.1
>
> Regards
> Paul
--
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PyMOL Principal Developer
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--
Check out the vibrant tech community on one of the world's most
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t; How can I get more sphere subdivision into the Collada export? I've tried
> sphere_quality 2 and cgo_sphere_quality 2, they seem to have no effect.
>
> --
> Gary Oberbrunner
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Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
=5.9 packages appeared in the
default anaconda channel, but unfortunately PyQt >5.6 doesn't handle the stereo
request properly on non-stereo hardware. Downgrading helps (conda install
pyqt=5.6).
Cheers,
Thomas
--
Thomas Holder
PyMOL Principal Developer
> (I want to use its .pdb file as an input for amber99ff in GROMACS.)
>
> Best regards
> -Roja
>
> On Thu, 10 May 2018, 00:47 Thomas Holder, <thomas.hol...@schrodinger.com>
> wrote:
> Hi Roja,
>
> This could be useful for you:
> 18 Nov 2017, NME and A
Then i didn't know how to add residue so i got help from taps and select ACE.
> But when i used this command,
> Edit last (name C)
> And then select NME from tabs, the NME were not connected to the last carbon
> and was completely separated.
> Would you please help me how s
t; --
> M.Sc. Andreas Tosstorff
> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
> Department Pharmazie
> LMU München
> Butenandtstr. 5-13 ( Haus B)
> 81377 München
> Germany
> Tel.: +49 89 2180 77059
>
>
--
Thomas Holder
PyMOL Principal Develo
> On Apr 24, 2018, at 7:17 PM, Yang Su <s...@crystal.harvard.edu> wrote:
>
> OK, thanks. If you don't mind, I can add it to the wiki:
> https://pymolwiki.org/index.php/Launching_From_a_Script
Sure, that would be great. Thanks a lot!
Cheers,
Thomas
--
Thomas Holder
PyMOL P
?
>
> Thanks,
> Yang
>
>
> On Mon, Apr 23, 2018 at 1:15 PM, Thomas Holder
> <thomas.hol...@schrodinger.com> wrote:
> Hi Yang,
>
> Yes it's possible to have independent instances. The API has actually been
> around for a long time. For some reason it was ne
--
>> fetch 1ESR, async=0
>> as cartoon
>> set cartoon_smooth_loops
>> spectrum
>> bg white
>> stereo anaglyph
>> ray 640,480
>> png demo.png
>> --
>>
>> Thank you for any input.
>>
>> Best,
>> Cod
cesses in a
> python script/jupyter notebook? Now with PyMOL 2.1 I can 'import pymol' and
> call a pymol.cmd function to start a backend process, but this is kind of
> 'global'. I'm looking for a way to manage multiple PyMOL sessions in
> parallel, each manipulating its own structure
is not possible
> to show ribbon as dashed/dotted lines.
>
> Thanks,
> Yang
>
>
> On Thu, Apr 19, 2018 at 1:54 PM, Thomas Holder
> <thomas.hol...@schrodinger.com> wrote:
> Hi Yang,
>
> Yes, since PyMOL 1.8.2 there is "cartoon dash". e.
,
>
> Is there an option to show the ribbon as dashed or dotted lines in pymol?
>
> Thanks,
>
> Yang
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant tech community on
ing the some.2fofc file was not found.
> volume abc, some.2fofc, 0, organic, 4., 1, 4
>
> Cheers, Paul
>
> Paul Steven Miller (PhD)
> Postdoctoral Researcher
> University of Oxford
> Wellcome Trust Centre for Human Genetics
> Division of Structural Biology
> R
es PyMol use to retrieve secondary structures from
> a pdb file (when the ss datas are not display in the file).
>
> I retrieved ss using dssp program, and for some pdb files, it shows strands
> or helix which are considered as loop by PyMol I guess.
>
> Thank you for your he
session = cmd.get_session()
>>
>> ... but my session object only includes one object, the cObjectMolecule. I'm
>> looking for it to include the graphics objects as well if that's possible.
>> Any hints?
>>
>>
>> --
>> Gary Oberbrunner -- CEO -- Dar
mistry
> School of Pharmacy | Te Kura Mātauraka Wai-whakaora
> University of Otago | Te Whare Wānanga o Otāgo
> PO Box 56 9054
> Dunedin | Ōtepoti
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--
Thomas Holder
PyMOL Princip
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