Menu
▾
▴
pymol-users — Collaborative support and tips for PyMOL users
You can subscribe to this list here.
| 2001 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(13) |
Nov
(22) |
Dec
(35) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2002 |
Jan
(33) |
Feb
(46) |
Mar
(56) |
Apr
(29) |
May
(56) |
Jun
(30) |
Jul
(64) |
Aug
(54) |
Sep
(86) |
Oct
(106) |
Nov
(50) |
Dec
(67) |
| 2003 |
Jan
(78) |
Feb
(98) |
Mar
(51) |
Apr
(95) |
May
(53) |
Jun
(103) |
Jul
(93) |
Aug
(64) |
Sep
(87) |
Oct
(93) |
Nov
(78) |
Dec
(86) |
| 2004 |
Jan
(83) |
Feb
(90) |
Mar
(64) |
Apr
(112) |
May
(103) |
Jun
(57) |
Jul
(101) |
Aug
(84) |
Sep
(92) |
Oct
(96) |
Nov
(86) |
Dec
(32) |
| 2005 |
Jan
(88) |
Feb
(108) |
Mar
(111) |
Apr
(107) |
May
(120) |
Jun
(134) |
Jul
(143) |
Aug
(129) |
Sep
(75) |
Oct
(171) |
Nov
(125) |
Dec
(65) |
| 2006 |
Jan
(95) |
Feb
(105) |
Mar
(114) |
Apr
(124) |
May
(87) |
Jun
(66) |
Jul
(88) |
Aug
(65) |
Sep
(71) |
Oct
(92) |
Nov
(94) |
Dec
(60) |
| 2007 |
Jan
(81) |
Feb
(84) |
Mar
(82) |
Apr
(68) |
May
(58) |
Jun
(80) |
Jul
(30) |
Aug
(47) |
Sep
(68) |
Oct
(92) |
Nov
(59) |
Dec
(17) |
| 2008 |
Jan
(69) |
Feb
(81) |
Mar
(60) |
Apr
(34) |
May
(47) |
Jun
(65) |
Jul
(46) |
Aug
(49) |
Sep
(84) |
Oct
(43) |
Nov
(33) |
Dec
(30) |
| 2009 |
Jan
(62) |
Feb
(48) |
Mar
(123) |
Apr
(73) |
May
(72) |
Jun
(69) |
Jul
(78) |
Aug
(72) |
Sep
(99) |
Oct
(82) |
Nov
(70) |
Dec
(53) |
| 2010 |
Jan
(112) |
Feb
(95) |
Mar
(127) |
Apr
(110) |
May
(135) |
Jun
(91) |
Jul
(91) |
Aug
(79) |
Sep
(136) |
Oct
(63) |
Nov
(38) |
Dec
(64) |
| 2011 |
Jan
(59) |
Feb
(109) |
Mar
(191) |
Apr
(130) |
May
(94) |
Jun
(90) |
Jul
(89) |
Aug
(127) |
Sep
(135) |
Oct
(113) |
Nov
(136) |
Dec
(140) |
| 2012 |
Jan
(158) |
Feb
(131) |
Mar
(151) |
Apr
(88) |
May
(121) |
Jun
(85) |
Jul
(82) |
Aug
(56) |
Sep
(55) |
Oct
(125) |
Nov
(87) |
Dec
(65) |
| 2013 |
Jan
(81) |
Feb
(64) |
Mar
(90) |
Apr
(77) |
May
(80) |
Jun
(92) |
Jul
(92) |
Aug
(70) |
Sep
(69) |
Oct
(60) |
Nov
(99) |
Dec
(50) |
| 2014 |
Jan
(89) |
Feb
(66) |
Mar
(52) |
Apr
(70) |
May
(68) |
Jun
(44) |
Jul
(68) |
Aug
(81) |
Sep
(152) |
Oct
(106) |
Nov
(74) |
Dec
(57) |
| 2015 |
Jan
(93) |
Feb
(48) |
Mar
(60) |
Apr
(107) |
May
(82) |
Jun
(64) |
Jul
(74) |
Aug
(38) |
Sep
(49) |
Oct
(99) |
Nov
(105) |
Dec
(51) |
| 2016 |
Jan
(68) |
Feb
(87) |
Mar
(55) |
Apr
(90) |
May
(68) |
Jun
(25) |
Jul
(25) |
Aug
(41) |
Sep
(35) |
Oct
(55) |
Nov
(24) |
Dec
(26) |
| 2017 |
Jan
(59) |
Feb
(49) |
Mar
(24) |
Apr
(50) |
May
(45) |
Jun
(63) |
Jul
(36) |
Aug
(26) |
Sep
(22) |
Oct
(23) |
Nov
(26) |
Dec
(29) |
| 2018 |
Jan
(17) |
Feb
(21) |
Mar
(30) |
Apr
(34) |
May
(24) |
Jun
(47) |
Jul
(65) |
Aug
(30) |
Sep
(24) |
Oct
(52) |
Nov
(21) |
Dec
(17) |
| 2019 |
Jan
(9) |
Feb
(39) |
Mar
(32) |
Apr
(22) |
May
(30) |
Jun
(69) |
Jul
(40) |
Aug
(48) |
Sep
(17) |
Oct
(26) |
Nov
(30) |
Dec
(19) |
| 2020 |
Jan
(32) |
Feb
(26) |
Mar
(16) |
Apr
(34) |
May
(50) |
Jun
(87) |
Jul
(51) |
Aug
(23) |
Sep
(25) |
Oct
(48) |
Nov
(32) |
Dec
(6) |
| 2021 |
Jan
(12) |
Feb
(31) |
Mar
(15) |
Apr
(31) |
May
(13) |
Jun
(13) |
Jul
(24) |
Aug
(9) |
Sep
(11) |
Oct
(28) |
Nov
(26) |
Dec
(25) |
| 2022 |
Jan
(47) |
Feb
(22) |
Mar
(22) |
Apr
(12) |
May
(4) |
Jun
(26) |
Jul
(17) |
Aug
(2) |
Sep
(13) |
Oct
(6) |
Nov
(13) |
Dec
(4) |
| 2023 |
Jan
(7) |
Feb
(6) |
Mar
(13) |
Apr
(2) |
May
(25) |
Jun
(13) |
Jul
(12) |
Aug
(10) |
Sep
(5) |
Oct
(13) |
Nov
(19) |
Dec
(7) |
| 2024 |
Jan
(3) |
Feb
(12) |
Mar
(1) |
Apr
(13) |
May
(11) |
Jun
|
Jul
(20) |
Aug
(4) |
Sep
(4) |
Oct
(5) |
Nov
(4) |
Dec
(6) |
| 2025 |
Jan
(16) |
Feb
(8) |
Mar
(10) |
Apr
(6) |
May
(13) |
Jun
(7) |
Jul
(4) |
Aug
(1) |
Sep
(2) |
Oct
(3) |
Nov
(4) |
Dec
|
|
From: Irwin S. <irw...@po...> - 2023-03-02 08:09:10
|
Hi, I would like to run the Align Python script found on the Align page of the PyMOLwiki (https://pymolwiki.org/index.php/Align). I've tweaked it slightly for my uses and it seems to run fine on PyMOL 2.5.0 but according to the wiki it should output a list of results (RMSD etc) in the internal feedback (or command prompt?), but it doesn't in my case. Does anyone know why? It does seem like there some missing lines to the script in order to achieve this. Apologies for the basic question! All the best, Irwin |
|
From: Petro <sub...@kh...> - 2023-02-18 16:55:04
|
Hi. I am curious if it is possible to run a local pymol and connect it to a remote pymol. I use pymol to process data on the remote machine via SSH without X forwarding using python and/or jupyter. I would like to show images on the local computer. Is it possible somehow without copying files to the local computer? Thanks. Petro. |
|
From: Gong, Z. <zg...@cu...> - 2023-02-14 02:54:22
|
Dear Pymol users, I am using the latest version of Pymol (version 2.5.4) and encountered this problem: I could open the .pse files ONLY through the “File” – “open…”, but NOT by double clicking on the .pse files. Could anyone please help what could be the problem and how to solve it? Many thanks in advance! Best, Zhen |
|
From: Olivia V. <oli...@gm...> - 2023-02-11 20:46:32
|
Hi,
I am using pymol to generate surface meshes from pdb source files. I would like to have the vertices in the same reference frame as the original pdb coordinates. However, when I save the obj file the object is centered at [0,0,0].
I tried to use the following code snippet to transform the surface, but it didn't do anything to the coordinates.
What am I doing wrong, or is the command not behaving how supposed to?
pymol.load(pdb_file)
view = list(pymol.get_view())
M = view[0:3] + [-view[12]] + view[3:6] + [-view[13]] + view[6:9] + [-view[14]] + view[12:15] + [1.0]
pymol.transform_selection("(all)", M, 0, 0, 0, 1)
pymol.set_view([1, 0, 0, 0, 1, 0, 0, 0, 1] + view[9:])
Any help would be greatly appreciated. If there is a way to avoid the centering at the loading stage, that would be awesome too.
Thanks
Olivia |
|
From: Harald L. <har...@fa...> - 2023-02-07 15:08:22
|
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
Dear list subscribers,<br>
<br>
we are very delighted to announce this year’s<br>
<br>
“35th Molecular Modelling Workshop (MMWS)”<br>
<a class="moz-txt-link-freetext" href="https://mmws2023.mgms-ds.de"
moz-do-not-send="true">https://mmws2023.mgms-ds.de</a><br>
<br>
taking place on Monday 13th to Wednesday 15th March 2023<br>
at the Friedrich-Alexander-Universität in Erlangen, Germany.<br>
<br>
The workshop, which is organised by the German Section of the
Molecular<br>
Graphics and Modelling Society (MGMS-DS e.V.), has a long history of<br>
giving young scientists (especially graduate students) the
opportunity<br>
to present their work and dive into discussions with each other and
the<br>
"older experts" of the field to gain valuable feedback from
academic, as<br>
well as industrial colleagues. Oral and poster contributions are
welcome<br>
from all areas of molecular modelling – from the life sciences,<br>
computational biology and chemistry, cheminformatics, to materials
sciences.<br>
<br>
After the forced Corona break, this year's meeting, for the first
time,<br>
offers a special session focussing on high-performance computing
(HPC)<br>
aspects in molecular modelling.<br>
<br>
Starting with the scientific program on Monday after lunch should
allow<br>
to avoid travelling on weekend keeping the expenses at a minimum.
Once<br>
again the location changed - we are now guest at the new Chemikum of
the<br>
Erlangen University at Nikolaus-Fiebiger-Strasse 10 (see<br>
<a class="moz-txt-link-freetext"
href="https://www.openstreetmap.de/karte/?zoom=17&lat=49.5782&lon=11.02864"
moz-do-not-send="true">https://www.openstreetmap.de/karte/?zoom=17&lat=49.5782&lon=11.02864</a>).
A<br>
hearty workshop dinner and a traditional joint evening event
complement<br>
the scientific program.<br>
<br>
The website <a class="moz-txt-link-freetext"
href="http://mmws2023.mgms-ds.de" moz-do-not-send="true">http://mmws2023.mgms-ds.de</a>
provides all necessary<br>
information about the meeting.<br>
<br>
####### Plenary Speakers #######<br>
We are very happy to announce that four outstanding researchers
already<br>
accepted our invitation to present a plenary lecture:<br>
<br>
Markus Reiher, ETH Zürich<br>
“Prospects of Quantum Computing for Chemistry”<br>
<br>
Paolo Carloni, Forschungszentrum Jülich<br>
"MiMiC: A new, highly scalable QM/MM interface for biophysical
applications"<br>
<br>
Peter Hildebrand, Universität Leipzig<br>
<br>
Oliver Koch, Universität Münster<br>
<br>
####### Poster and Lecture Awards #######<br>
As in the past years, there will be two poster awards of EUR 100
each<br>
and three lecture awards for the best contributed oral
presentations:<br>
<br>
1st winner: Travel bursary to attend the Young Modeller's Forum
(YMF) in<br>
London, UK, plus a recommendation for a speaker slot option at YMF<br>
(travel expenses are reimbursed up to EUR 500)<br>
2nd winner: EUR 200 travel expenses reimbursement<br>
3rd winner: EUR 100 travel expenses reimbursement<br>
<br>
Only undergraduate and graduate research students qualify for the
poster<br>
and lecture awards.<br>
<br>
####### Registration and poster/talk submission #######<br>
Submit talk and/or poster titles via the registration form
accessible on<br>
the workshop website <a class="moz-txt-link-freetext"
href="https://mmws2023.mgms-ds.de/index.php?m=register"
moz-do-not-send="true">https://mmws2023.mgms-ds.de/index.php?m=register</a><br>
The deadline for all submissions is February 26th, 2023.<br>
<br>
####### NHR@FAU meeting #######<br>
The Erlangen National High Performance Computing Center (NHR@FAU),
which<br>
is supporting our meeting, organizes it's first Colloquium and
Results<br>
Symposium. It will take place on Wednesday afternoon and Thursday,<br>
directly after our event, at exactly the same venue. If you are<br>
interested in Atomistic Simulations on High Performance Computing<br>
clusters, consider to extend your stay in Erlangen and also attend
the<br>
NHR@FAU meeting for free! For further information have a look at<br>
<a class="moz-txt-link-freetext" href="https://hpc.fau.de/"
moz-do-not-send="true">https://hpc.fau.de/</a><br>
<br>
If you have any questions, do not hesitate to contact us via<br>
<a class="moz-txt-link-abbreviated moz-txt-link-freetext"
href="mailto:mm...@mg..." moz-do-not-send="true">mm...@mg...</a>
.<br>
We are looking forward to meeting you in Erlangen!<br>
<br>
On behalf of the workshop organising team<br>
- Harald Lanig, Chairman of the MGMS-DS e.V. (<a
class="moz-txt-link-freetext" href="http://www.mgms-ds.de"
moz-do-not-send="true">http://www.mgms-ds.de</a>)<br>
<br>
<br>
<pre class="moz-signature" cols="72">--
PD Dr. rer. nat. Harald Lanig (Dipl.-Chem.)
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Zentrum für Nationales Hochleistungsrechnen Erlangen (NHR@FAU)
NHR@FAU Geschäftsstelle am Regionalen Rechenzentrum Erlangen (RRZE)
Martensstrasse 1, 91058 Erlangen, Germany
<a class="moz-txt-link-abbreviated moz-txt-link-freetext" href="mailto:har...@fa..." moz-do-not-send="true">har...@fa...</a> - hpc.fau.de</pre>
</body>
</html>
|
|
From: Mooers, B. H.M. (HSC) <Bla...@ou...> - 2023-02-06 20:02:02
|
Hi Chao, Try issuing the following command at the PyMOL> prompt: set display_scale_factor, 2 It enlarges the font of the sequence in the viewport and the text in the internal GUI. It only takes whole numbers. Try larger intergers; you can always return to 2 or 1. It is useful when giving workshops and lectures about PyMOL. It may not do all that you require. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function COBRE in Structural Biology: https://www.ou.edu/structuralbiology ________________________________ From: Chao Chen <bio...@gm...> Sent: Monday, February 6, 2023 12:41 PM To: pym...@li... <pym...@li...> Subject: [EXTERNAL] [PyMOL] Question about formatting font size Dear Users, I found in pymol layout somehow characters including protein sequence letters become very small. Not sure what I have done. Any ideas of changing to a bigger font? Thanks a lot in advance! Kind regards, Chao |
|
From: Chao C. <bio...@gm...> - 2023-02-06 18:41:56
|
Dear Users, I found in pymol layout somehow characters including protein sequence letters become very small. Not sure what I have done. Any ideas of changing to a bigger font? Thanks a lot in advance! Kind regards, Chao |
|
From: Qingping Xu <qx...@an...> - 2023-01-30 19:02:23
|
This is reminder that the registration for the upcoming CCP4/APS school will close in two days (1/31/2023). If you plan to attend, please submit your application asap. Thanks. Charles, Andrey, Garib and Qingping On 1/23/23 14:43, Qingping Xu wrote: > This is a reminder for students interested in attending the upcoming > onsite CCP4/APS school, please submit your applications. > > Thanks > > Charles, Andrey, Garib and Qingping > > > On 1/3/23 08:37, Qingping Xu wrote: >> Dear colleagues, >> >> Happy new year! >> >> This is a reminder that the registration is open for the upcoming >> 2023 CCP4/APS school. Please note this year school is earlier than >> the usual summer date (before the APS upgrade starting in middle >> April). Please apply if you are interested in attending in person, or >> forward to students who may be interested. >> >> Thanks >> >> >> Charles, Andrey, Garib and Qingping >> >> >> On 10/20/22 12:13 PM, Qingping Xu wrote: >>> Dear Colleagues, >>> >>> We are pleased to announce the 15th annual CCP4/APS crystallographic >>> school “From data collection to structure refinement and beyond” >>> will be held on March 27th to April 3rd, 2023 at the 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-2023/index.php. This will be our >>> first post-COVID in person workshop, scheduled before the APS >>> upgrade shutdown. >>> >>> >>> Dates: March 27 through April 3, 2023 >>> 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 draft >>> program can be found at the School website. >>> >>> Applicants: The workshop strongly encourages students who need >>> expert help with difficulties/challenges in their own projects. >>> Graduate students, postdoctoral researchers and early-career >>> faculty, along with commercial/industrial researchers are encouraged >>> to apply. Only about 20 applicants will be selected for participation. >>> >>> Application: Application deadline is Jan 31th, 2023. To apply, >>> visit https://www.ccp4.ac.uk/schools/APS-2023/application.php >>> >>> Fees: There is a $500 participation fee for the selected academic >>> students and $1500 for industrial researchers. No credit card will >>> be required for registration, students who are selected to >>> participate will be contacted to pay. The students will be >>> responsible for their transportation and lodging. The workshop >>> organizers can assist in making 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, Andrey, Garib and Qingping >>> >>> ######################################################################## >>> >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a >>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are >>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a >> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ |
|
From: Qingping Xu <qx...@an...> - 2023-01-23 20:58:32
|
This is a reminder for students interested in attending the upcoming onsite CCP4/APS school, please submit your applications. Thanks Charles, Andrey, Garib and Qingping On 1/3/23 08:37, Qingping Xu wrote: > Dear colleagues, > > Happy new year! > > This is a reminder that the registration is open for the upcoming 2023 > CCP4/APS school. Please note this year school is earlier than the > usual summer date (before the APS upgrade starting in middle April). > Please apply if you are interested in attending in person, or forward > to students who may be interested. > > Thanks > > > Charles, Andrey, Garib and Qingping > > > On 10/20/22 12:13 PM, Qingping Xu wrote: >> Dear Colleagues, >> >> We are pleased to announce the 15th annual CCP4/APS crystallographic >> school “From data collection to structure refinement and beyond” will >> be held on March 27th to April 3rd, 2023 at the 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-2023/index.php. This will be our >> first post-COVID in person workshop, scheduled before the APS upgrade >> shutdown. >> >> >> Dates: March 27 through April 3, 2023 >> 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 draft >> program can be found at the School website. >> >> Applicants: The workshop strongly encourages students who need expert >> help with difficulties/challenges in their own projects. Graduate >> students, postdoctoral researchers and early-career faculty, along >> with commercial/industrial researchers are encouraged to apply. Only >> about 20 applicants will be selected for participation. >> >> Application: Application deadline is Jan 31th, 2023. To apply, visit >> https://www.ccp4.ac.uk/schools/APS-2023/application.php >> >> Fees: There is a $500 participation fee for the selected academic >> students and $1500 for industrial researchers. No credit card will be >> required for registration, students who are selected to participate >> will be contacted to pay. The students will be responsible for their >> transportation and lodging. The workshop organizers can assist in >> making 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, Andrey, Garib and Qingping >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a >> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ |
|
From: Jared S. <jar...@co...> - 2023-01-19 21:54:20
|
Hi Petro - This is the object's "title" attribute, and can be accessed using the Properties Inspector <https://pymolwiki.org/index.php/Properties_Inspector> in the top right part of the GUI, as well as read or edited via the `get_title <https://pymolwiki.org/index.php/Get_Title>` or `set_title <https://pymolwiki.org/index.php/Set_title>` commands, respectively (e.g. `get_title group1-out, 1`). Hope that helps. Cheers, Jared On Thu, Jan 19, 2023 at 5:09 AM Petro <sub...@kh...> wrote: > Hi again. > I got a proposal to use the action menu, but it is a bit different. > https://photos.app.goo.gl/GkCyr67JfWSDKUU57 > Please take a look at this photo. > I am interested in reading and editing the information in green. > Thanks. > Petro. > > > On Wed, 18 Jan 2023 at 13:44, Petro <sub...@kh...> wrote: > >> Hi, list. >> When I load the mol2 file, the title of the molecule is shown near the >> object name in green in the internal GUI. Is there a way to read it? Maybe >> even edit it? >> Thanks. >> Petro. >> >> _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
|
From: Petro <sub...@kh...> - 2023-01-19 19:40:38
|
Hi Jared. Have not tried yet, but it looks like you have solved the problem for me. Thanks. Petro. On Thu, 19 Jan 2023, 8:13 pm Jared Sampson, <jar...@co...> wrote: > Hi Petro - > > This is the object's "title" attribute, and can be accessed using the Properties > Inspector <https://pymolwiki.org/index.php/Properties_Inspector> in the > top right part of the GUI, as well as read or edited via the `get_title > <https://pymolwiki.org/index.php/Get_Title>` or `set_title > <https://pymolwiki.org/index.php/Set_title>` commands, respectively (e.g. > `get_title group1-out, 1`). > > Hope that helps. > > Cheers, > Jared > > On Thu, Jan 19, 2023 at 5:09 AM Petro <sub...@kh...> wrote: > >> Hi again. >> I got a proposal to use the action menu, but it is a bit different. >> https://photos.app.goo.gl/GkCyr67JfWSDKUU57 >> Please take a look at this photo. >> I am interested in reading and editing the information in green. >> Thanks. >> Petro. >> >> >> On Wed, 18 Jan 2023 at 13:44, Petro <sub...@kh...> wrote: >> >>> Hi, list. >>> When I load the mol2 file, the title of the molecule is shown near the >>> object name in green in the internal GUI. Is there a way to read it? Maybe >>> even edit it? >>> Thanks. >>> Petro. >>> >>> _______________________________________________ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pym...@li... >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > |
|
From: Petro <sub...@kh...> - 2023-01-19 10:07:45
|
Hi again. I got a proposal to use the action menu, but it is a bit different. https://photos.app.goo.gl/GkCyr67JfWSDKUU57 Please take a look at this photo. I am interested in reading and editing the information in green. Thanks. Petro. On Wed, 18 Jan 2023 at 13:44, Petro <sub...@kh...> wrote: > Hi, list. > When I load the mol2 file, the title of the molecule is shown near the > object name in green in the internal GUI. Is there a way to read it? Maybe > even edit it? > Thanks. > Petro. > > |
|
From: Petro <sub...@kh...> - 2023-01-18 12:45:07
|
Hi, list. When I load the mol2 file, the title of the molecule is shown near the object name in green in the internal GUI. Is there a way to read it? Maybe even edit it? Thanks. Petro. |
|
From: Jason W. <Jas...@ne...> - 2023-01-09 10:25:14
|
Hi all, This is a long shot. But I am having problems fitting a model to a cryoEM map with bond modifications completed in pymol and I am hoping someone can help. I downloaded a structure from the PDB database, and I am adding two bonds between nucleotides. However, these bonds do not appear to save correctly to mmCIF or PDB, often being lost as they do not show up in ChimeraX. When trying to open these files again in pymol, I can see random things like a hydrogen with two bonds in place of the new bond I made. The modifications appear to save okay to mol2, but phenix refuses to use the file afterwards anyway. I feel like I am missing a step because phenix asks for restraints and when I try to run elbow, it just crashes with the PDB and mmCIF files. The Mol2 file does not load in phenix and just crashes phenix. I have gotten the mol2 file to open in chimeraX and then save as pdb afterwards. I did generate restraints for this file, but it completed this without the actual modifications I made so was pointless. So, I am kind of stumped right now. Has anyone had any experience with creating new bonds in PDB files and saving them for use with fitting to cryoEM maps and refinement? Thanks, Jason Woodgate Newcastle University. |
|
From: <496...@qq...> - 2022-12-31 05:22:29
|
I am a student. I applied for a free download voucher on the website, but I haven't sent an email to me. I hope you can reply as soon as possible. Thank you！！！ |
|
From: Islam, S. [GDCBS] <sa...@ia...> - 2022-12-28 17:37:11
|
Hi, I wanted to register using giving my credentials and email id to Pymol for educational purpose on 25th December. I did not get any registration confirmation email. I checked my inbox and Junk Folder on outlook. No email from Pymol. Then I emailed Pymol regarding the problem @he...@sc.... I still did not get a reply. Could you help? --------------- Saiful Islam Interdepartmental Plant Biology, Ph.D. Program Graduate Research Assistant, Aung Lab Dept. of Genetic, Development, and Cell Biology Iowa State University 3339-7 ATRB, 2213 Pammel Dr, Ames, IA 50011-4009 |
|
From: wenchao z. <zha...@gm...> - 2022-12-09 16:50:04
|
Dear Pymol users, I have a question about transparency. I would like to transparent both the cartoon and the surface to highlight the sticks, but when I transparent both of them, the cartoon will disappear, how do you solve this? Thank you in advance! |
|
From: Yogesh S. <yog...@gm...> - 2022-12-05 10:20:34
|
hi all, I am trying to graph the diversity of amino acids on both planes of the aromatic side chain of tryptophan, but not getting any hint of where to start. Is there any way to map 3D coordinates on a 2d plot? Please suggest. * with regards* *Yogesh Sharma* |
|
From: Xiang-Jun Lu <3d...@gm...> - 2022-11-30 04:29:18
|
Dear list members, I thought it is worth noting that the 2x12 cover images of the *RNA Journal* in 2021 and 2022 have all been generated by the Nucleic Acid Database ( ndbserver.rutgers.edu) using DSSR and PyMOL. See the composite at http://docs.x3dna.org/images/RNAcovers-NDB-dssr-pymol.png and the December 2022 issue at https://rnajournal.cshlp.org/content/28/12.cover-expansion Users can easily generate such highly simplified, yet informative images of nucleic acid structures using http://skmatic.x3dna.org Best regards, Xiang-Jun -- Xiang-Jun Lu (Ph.D.) Email: xia...@x3... Web: http://x3dna.org/ Forum: http://forum.x3dna.org/ |
|
From: Mooers, B. H.M. (HSC) <Bla...@ou...> - 2022-11-27 14:00:23
|
Hi Prathvi, You will find answers to the first three questions on the PyMOL wiki: https://pymolwiki.org/index.php/Selection_Algebra Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function COBRE in Structural Biology: https://www.ou.edu/structuralbiology ________________________________ From: Prathvi Singh <pr...@ii...> Sent: Wednesday, November 23, 2022 1:16 AM To: pym...@li... <pym...@li...> Subject: [EXTERNAL] [PyMOL] Questions regarding selection Hi, I have a few questions regarding selection command for which I am unable to find the answers: How to select, say 100th and 120th residue of chain-A and 50th residue of chain-B? How to select all the alanine residues of chain-A and glycine residues of chain-B? How to count the total number of selected residues? How to display residue information on hovering the mouse over it like in UCSF chimera? Thanks in advance -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016 |
|
From: Prathvi S. <pr...@ii...> - 2022-11-23 07:36:38
|
Hi, I have a few questions regarding selection command for which I am unable to find the answers: How to select, say 100th and 120th residue of chain-A and 50th residue of chain-B? How to select all the alanine residues of chain-A and glycine residues of chain-B? How to count the total number of selected residues? How to display residue information on hovering the mouse over it like in UCSF chimera? Thanks in advance -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016 |
|
From: Jarrett J. <jar...@sc...> - 2022-11-18 20:07:47
|
Hello, https://www.pymolwiki.org/index.php/Load_traj outlines the steps to load gromacs (two steps: load gro structure file, then xtc trajectory files) and other types of trajectory files into PyMOL. Hope this helps, Jarrett J. On Fri, Nov 18, 2022 at 11:03 AM Khoroshyy Petro <kho...@gm...> wrote: > Hi. > Is there a way to load gromacs and amber trajectory? > Thanks > Petro > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL |
|
From: Natalia <N.M...@hh...> - 2022-11-17 15:44:32
|
Hello Pymol community! I would like to be able to render high quality images of a surface representation of large structures, such as the ribosome. However when I set the surface quality to 2, on my machine it takes ages to get the surface representation. Would a GPU be of any use to speed up this step, or is it used only in the rendering step? Which would be the hardware requirements to speed this up and make it run more smoothly? On our server (Linux) this process uses really little RAM and 1 thread, and after 2 hours it gives out the error message: CGO-Error: CGOCombineBeginEnd: invalid op=0x00 inside BEGIN/END Does anyone know what it means? I really wasn´t able to detect which hardware component is the bottleneck. I would be very grateful if someone could help me out! Cheers, Natalia |
|
From: Khoroshyy P. <kho...@gm...> - 2022-11-17 10:17:10
|
Hi. Is there a way to load gromacs and amber trajectory? Thanks Petro |
|
From: Colin D. <Col...@uw...> - 2022-11-15 18:20:59
|
During mutagenesis dashed yellow lines appear from the main chain of the new aa with distances attached and they remain when moving through the various rotamer states. Is there a way of hiding these lines and labels? |
115 messages has been excluded from this view by a project administrator.
