installer (nvidia...6629pkg2.run) is getting confused as to which
kernel is running.
Has anyone else had these issues/knows any hints.
Many thanks in advance
J
--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
NMR Spectroscopy, Utrecht University
Padualaan 8, 3584 CH Utrecht, The Netherlands
_kos...@nmr.chem.uu.nl_
phone: +31-30-2532875
fax: +31-30-2537623
:-)
--
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Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Pukenga
=6595alloc_id=14396op=click
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Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New
Hi folks,
I have recently installed pymol on a friends ibook and it all works
fine...but there seems to be no external GUI (as seen on PC and Linux
versions). Is it missing on OSX or is my install flawed? It does make it
a little easier to use for the novice.
Cheers
Joel
--
Joel Tyndall
Thanks folks,
I did have the hybrid version running but I have now installed the
Macpymol version which seems a whole lot easier to install, ie it does
it itself!
Thanks for your help
J
--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New
!
Cheers
J
--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa
Ph / Waea +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034
its supposed to when you double click on this ie open (or use the
hyperlink from powerpoint).
It does however work when you open the file from within pymol but
doesn't go full screen but opens just like a .pse file.
Any suggestions would be helpful.
Regards
Joel
--
Joel Tyndall, PhD
So whilst I'm picking your collective brains, how would I set up a
superimposition using say 4 different residues usingthe backbones or ca
atoms? ie two from each separate chain of the homodimer?
Thanks again
J
--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO
to get up to
speed, fast. http://ads.osdn.com/?ad_idt77alloc_id492op=click
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Lecturer
National School
,
suggestions will be appreciated.
Thanks.
Regards,
Madhavi Kolli
Graduate Student
UMass Medical School Worcester
--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o
://lists.sourceforge.net/lists/listinfo/pymol-users
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Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa
Ph / Waea
@lists.sourceforge.net
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Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa
Ph
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
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Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka
badly rendering
pymol and any other program essentially useless (flicker is the whole
screen and the desktop shape changes to a trapezoid shape).
Any body know how to fix this. Have people tested this driver? Should I
load an earlier driver?
Many thanks
Joel
--
Joel Tyndall, PhD
Lecturer
system).
Anyway thanks again
J
--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa
Ph / Waea +64 3
Hi folks,
I was a little pre-emptive. The flicker is back! so no solution yet.
J
--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913
://lists.sourceforge.net/lists/listinfo/pymol-users
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Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa
Ph / Waea +64 3
(i.e. other
structures that amino acids inside of a protein). Any visualization similar
to electron density would be also useful.
Thanks!!
lena
--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Pukenga
Te Kura
Hi folks,
hopefully an easy solution but how do I read all the molecules (scroll
thru) in a multi-sdf file or mol file. I have tried the split states
command but that only reads the first molecule.
Any help would be appreciated.
J
--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
Hi all,
I'm not sure if this has been asked before and I'm not sure if its
possible...but here goes anyway. Is there a way to print/export the
sequences in the viewer window? It would be an easy way to translate
actual secondary structure to a sequence alignment
Thanks
J
--
Joel Tyndall
Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642
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National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Pukenga
Te Kura
--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa
Ph / Waea +64 3 4797293
Fax / Waeawhakaahua +64
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Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Pukenga
Te Kura Taiwhanga
:
Hi all,
in pymol is it possible to align states rather than object. I mean, I
have loaded a pdb file with n-structures and I'd like to align each of
them on the first one of the bundle.
Thanks in advance
Regards
andrea
--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University
://lists.sourceforge.net/lists/listinfo/pymol-users
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Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand
Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa
Ph
the files from my Linux machine (all works fine
there) and the problem is on the PC. And the docked poses are generated
from GOLD.
Any help?
J
--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand
Pukenga
Te
_
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand
Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa
Ph / Waea
Hi there,
The gallery is currently in 2D format. Any plans to generate 3D galleries?
J
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand
Pukeka Matua
Te Kura Taiwhanga
Hi folks,
Just updated my pymol version to 1.1 on my linux boxes and I get an error
floating point.
I am running centos 4.6 32 bit...any suggestions? I've got nothing. 1.0r2 works
fine.
J
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National
Hi Warren,
I notice the FAQ link is missing from the website. I found the page but no
link, was looking so my students can cite pymol appropriately. Will it be
reinstated?
Cheers
J
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa
Ph / Waea
. [show the sequence - S
button bottom right, move the slider to the end of the protein (usually) and
select the metal(s) show spheres of selection]
Hope this helps
J
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University
others cab see the
results
Regards
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa
Ph
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56
Hi Bala,
Start with split_states your_object. If its an NMR structure with multiple
solutions, then this will make each a separate object. I find this much
easierto deal with. Also works for Biological units with multiple units
involved.
J
_
Joel Tyndall
You can also download the sequence directly from the pdb
J
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803
to the older versions.
I can provide files if required
Is the only option to generate educational presentations for my lectures
using the edu version?
Thanks
J
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University
PS is it possible to run two versions at once on a PC (a quick test failed)
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008
status
quo.
Thanks for any help
J
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te
with pymol. (I want to
run modeler, sybyl and gold also ) This is not to mention the fact that the
kernel doesn't have wireless or Ethernet drivers.
Should I downgrade or persist.
Many thanks for comments
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
Thanks folks, will start with FC11
J
From: Joel Tyndall [mailto:joel.tynd...@otago.ac.nz]
Sent: Tuesday, 15 December 2009 4:33 p.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Slightly off topic
Hi folks,
Sorry for the off topic post. I have just got a new whizz bang laptop and I'm
A to match the numbers of
chain B (if it doesn't already match)
I'm pretty sure this will give you what you want. It is at least one method
Joel
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin
Hi,
Yeah I have a similar issue and have been meaning to post it. On windows 7
following minimization, the viewer doesn't update when you open it again, no
menus either. Using PyMOL 1.2r2
Looking forward to a solution
J
_
Joel Tyndall, PhD
Senior Lecturer
Try setting your Pymol viewer to square dimensions first:
Viewport 600,600
Then try the ray command
This should work
Joel
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New
it with VMWare player but
virtual box looks possible (not sure though)
Comments appreciated
J
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka
Showlines or sticks this does not then
show them. I'm sure there is a background (python) setting to adjust this but
is it possible to include the carbonyl's in question with the initial preset?
HIV protease is a good example to show this.
Cheers
Joel
_
Joel Tyndall
generate such a peptride,
save it then reopen in Pymol, extra bonds are drawn between N-H and O=
indicating the close proximity. Whilst I realise Pymol is not currently
designed to Model structures, could this be updated.
Cheers
Joel
_
Joel Tyndall, PhD
Senior
the excellent graphics
I am using both a phenix generated mtz (works with Fileopen mtz) and a ccp4
generated one (File open)
Cheers
Joel
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56
Hi Martin,
Whilst I have no competence what so ever in scripting, I believe the
measurement wizard does offer you the torsion angle option only it is listed
as a dihedral.
Hope this helps
Joel
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
A quick google search found this:
http://www.nyu.edu/pages/mathmol/library/water/
hope this helps
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
-10.428 23.682 1.00 11.53 A
C
ATOM 56 OVAL A 6 -9.347 -11.540 23.573 1.00 12.73 A
O
Where the AVAL and BVal correspond to different orientations.
Hope this helps
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56
Hi Nat,
In mine its
C:\Program Files\PyMOL\PyMOL\PyMOL.exe
Hope this helps
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56
Hi Shane,
I think I meant weblogo which shows frequency of amino acids
e.g. http://weblogo.berkeley.edu/
Sorry for the confusion
J
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin
//a/tyr61/cb, 1abc//a/tyr61/cb, 1xyz//a/tyr61/ca,
1abc//a/tyr61/ca, 1xyz//a/tyr61/c, 1abc//a/tyr61/c
Or something along those lines.
Hope this helps
Joel
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO
the pairfitting actually I could
do this easily by command line but I have 100 molecules so I'm not sure how
to script this.
Any help would be welcome
Cheers
Joel
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University
Hi Anika,
If you open molecules in the same window then yes they will be the same scale.
However if you open two different molecules in different windows, the view will
not necessarily be to scale (e.g. small molecule drug compared to a protein).
Hope this helps
Joel
-Original
Hi Martin,
I might be missing something but a little more information might help as to
what you want to do. agreed, a file extension can be changed to anything but
viewing the text file should tell you the type (of coordinate file). If you are
doing this in batch mode then I guess a script
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
Ph: +64 3 479 7293
--
Everyone
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
Ph: +64 3 479 7293
--
Keep yourself connected to Go Parallel
Hi list,
With the myriad of colours in Pymol, I tend to forget which shade of what I
have used. Is there a way/command to print the colour I have used to colour
object X?
Cheers
Joel
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School
but not least, there is the psico.querying.get_color function in the PSICO
module :)
Cheers,
Thomas
Joel Tyndall wrote, On 01/23/13 02:04:
Hi list,
With the myriad of colours in Pymol, I tend to forget which shade of
what I have used. Is there a way/command to print the colour I have
used
That's pretty slick.
Alternatively you can delete the drawn bonds using the builder module. Then
show nb_sphere for the Fe atom. If you have access to the CSD I would grab one
from there
Hope this helps
From: Troels Emtekær Linnet [mailto:tlin...@gmail.com]
Sent: Tuesday, 12 February 2013
Hi Matthias, I can at least try and answer some of your questions:
1. You can simply click on the command button (rhs side grey window...
Command Builder Volume) to get back to the command info you want.
Alternatively type in your commands into the viewer window and use escape to
see
mustang already
Cheers
Joel
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
Ph: +64 3 479 7293
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
Ph: +64 3 479 7293
--
Minimize network downtime
Try modeller
http://salilab.org/modeller/about_modeller.html
From: yp sun [mailto:sunyep...@yahoo.com.cn]
Sent: Tuesday, 7 May 2013 1:58 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] repair the missing loop in crystal structure
Dear pymol users,
Are there anyone know how to
Hi Bob,
This is probably not the slickest way to do this but generally I think it is
one surface one object, so in a simple case of a peptide bound to a protein, I
would select the peptide chain (right click in the viewer) and extract that
selection to a new object and then you can generate
Subject: RE: [PyMOL] Possible hydrogen addition bug
Hi all,
I believe this would be as a result of the pdb file not containing the
hybridisation information. When you manually change that bond to be double
(using the builder module) and then add hydrogens it is correct. This is not an
Hi Jerome,
I am guessing you would be referring to the cartoon representation of the cycic
peptide. This is only a workaround but I would usually display the sticks of
the covalently linked N-and C termini (main chain atoms). I feel this provides
the viewer a better understanding of the
Haddock?
-Original Message-
From: Lapolla, Suzanne M (HSC) [mailto:suzanne-lapo...@ouhsc.edu]
Sent: Tuesday, 8 April 2014 7:12 a.m.
To: pymol-users@lists.sourceforge.net
Cc: thomas.hol...@schrodinger.com
Subject: Re: [PyMOL] manual superposition with pymol--and another question
This
Wishing you all the best Jason, it has been fantastic to be involved with this
bb with you as the key guy. Always there to answer the questions
From: Jason Vertrees [mailto:jason.vertr...@gmail.com]
Sent: Thursday, 24 April 2014 9:00 p.m.
To: pymol-users; ccp...@jiscmail.ac.uk
Subject: [PyMOL]
_
Joel Tyndall, PhD
Associate Professor in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
Ph: +64 3 479 7293
no issues.
Current version is 1.7.6.2
Any idea how to fix this? Might be my hardware but just wondering if others see
this or there is a fix?
J
_
Joel Tyndall, PhD
Associate Professor in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box
That would be great, my standard is open file, cartoon, ligand sticks
Great idea
-Original Message-
From: Thomas Holder [mailto:thomas.hol...@schrodinger.com]
Sent: Tuesday, 9 February 2016 5:52 AM
To: Ivan Vulovic ; Schubert, Carsten [JRDUS]
Cc:
not convinced it works on a
windows 8 machine either but it they do work on windows 7 on 1.7.2.0 release.
When upgraded to 1.8.0 on windows 7 PyMOL crashes. Is there any fix for this or
am I stuck with the problem?
J
Joel Tyndall | BSc(Hons) PhD
Associate Professor in Medicinal Chemistry
New Zealand’s
Hi,
Select the one you want e.g. right click, chain select. Under the selection,
Action > modify > invert > within object..
Or you can select using the sequence viewer
Hope this helps
Joel
From: Mohammad Goodarzi [mailto:mohammad.goda...@gmail.com]
Sent: Friday, 23 June 2017 8:20 AM
To:
It can easily be done in PyMOL
Select your molecule, then in the right side select A(Action)->Generate->Vacuum
Electrostatic
Or there are plenty of tutorials on the web for APBS
Hope this helps
J
From: Clarisa Alvarez
Sent: Thursday, 28 June 2018 3:05 AM
To:
Hi Markus,
I am not aware of this function in pymol but would be interested in one being
developed.
J
-Original Message-
From: Markus Heller
Sent: Friday, 24 August 2018 6:28 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Display metal coordination
Hi all,
Is there a way
Hi Markus,
Is there still a gap (between atoms and cartoon) when you turn on the backbone
residues in question?
J
From: Markus Heller
Sent: Thursday, 6 September 2018 6:26 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Hbond to backbone cartoon
Hi all,
what's the best way to show
Hi folks,
Is pymol able to protonate an amine e.g. morphine i.e. when you add hydrogens
to a small molecule, ensure that the amine is charged (at it would be at
physiological pH?
I have not been able to do it using the GUI.
Cheers
Joel
Joel Tyndall | BSc(Hons) PhD
Associate Professor
Hi,
You can use the pair-ftt function to better overlay the ligands.
You can also display the torsion angles:
In 3-button editing mode, hold control down (PC) and right click on the bond in
question.
Not sure how to do this command line
Hope this helps
J
From: puneet garg
Sent: Friday, 12
Hi Maryam,
You can easily align two proteins in Pymol to compare their structures. Read
both protein structures into the same window under the action option, choose
align and select which one you want. E.g align to molecule (via alpha carbons)
Hope this is what you wanted
J
Hi Neena,
Use the command “split_states clusters”, just type it into the command line
J
From: Neena Susan Eappen
Sent: Monday, 8 June 2020 10:01 am
To: pymol-users
Subject: [PyMOL] View two proteins from one pdb file
Hello PyMOL users,
I have a PDB file with coordinates for two proteins
Hi,
I got interested so had a quick look. There is a user manual in the
doc/directory on github
https://github.com/schlessinger-lab/pyvol
Should give you details of how to use it
Hope this helps
J
From: ALBAYATI SAMAH HASHIM KHALEEL / UPM
Sent: Wednesday, 18 November 2020 5:40 AM
To:
I can only but agree with al of these comments! Thanks for the support and god
luck with the future Thomas.
PyMOL has been my go to software for probably close to 20 years !
Regards
Joel
-Original Message-
From: Jason Key
Sent: Saturday, 1 May 2021 3:15 AM
To: Thomas Holder
Cc:
Hi Jessica,
Generally secondary structure is extracted from a pdb file and PyMol would read
this.
e.g.
HELIX1 1 GLY A 86 THR A 91 1 6
HELIX2 2 GLY B 86 THR B 91 1 6
SHEET1 A 4 GLN A 2 THR A 4
Please ignore my previous message!
File > Export alignment!
From: Joel Tyndall
Sent: Tuesday, 19 October 2021 4:24 pm
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Export aligned sequence
Hi folks,
I have two proteins aligned in PyMOL. Is there a way to export the resulting
seque
Hi folks,
I have two proteins aligned in PyMOL. Is there a way to export the resulting
sequence alignment?
I have had a very brief look at structural alignment servers but PyMOL seems to
give me what I want structurallyand sequence wise
J
Joel Tyndall | BSc(Hons) PhD
Associate Professor
Have you tried superimposing the loop (or the main chain of the terminal
fragments? You could then export the moved loop and edit the pdb
J
From: zeinab masoomi
Sent: Monday, 22 November 2021 9:52 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] fusing structures
Hi
I want to fuse a
Hi Enrico,
Which docking protocol are you using as this may already have RMSD to a
reference ligand and presentation of best poses (based on scoring)
Joel
-Original Message-
From: Enrico Martinez
Sent: Friday, 25 March 2022 2:11 AM
To: pymol-users
Subject: [PyMOL] Analysis of
I agree with Tim, PyMOL simply adds bonds based on the geometry of the
structure. The salt bridge is very close. The "problem" (if any) lies with the
crystal structure coordinates
-Original Message-
From: Timofey Tyugashev
Sent: Tuesday, 6 September 2022 3:17 PM
To:
typing would be such that it recognises the appropriate ionised state (along
with the residue)
Joel
Joel Tyndall | BSc(Hons) PhD
Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand
Have you tried .mol2 files. I would expect Maestro to recognise that and it
should include bond order etc
J
Joel Tyndall, PhD
Associate Professor in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http
Joel
Joel Tyndall | BSc(Hons) PhD
Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Website | pharmacy.otago.ac.nz
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