., 10 sty 2025 o 18:22 Patrick Loll <pjl...@gmail.com> napisał(a):Happy New Year, Everyone,
I have a question about the “cleaning syringe” that is sold for DI water systems such as the Barnstead Nanopure (when one replaces the cartridge, one injects the contents of this 60-mL syringe in
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-------
Patrick J. Loll, Ph. D. (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 1
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tions you're working with - find some new
ones!
Good luck,
Patrick
On Fri, Dec 6, 2024 at 2:18 AM 白雪慧 wrote:
> Thank you very much for your reply to my question on how to optimize
> microcrystal. In response to your suggestions and questions, I would like
> to make the following rep
XQuartz 2.8.5 to 2.8.3 to 2.8.1 to 2.8.0
(restarting after installing each version), and get the same behavior with
each. And I don’t have ScreenTime turned on.
Any thoughts?
Much obliged,
Pat
---
Patrick J
the M4 machines?
Speculation welcome.
Cheers,
Pat
—
Patrick J. Loll, Ph. D. (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 1
>
> Cait Dennis
> Lecturer, HullYork Medical School, University of York, UK.
>
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patr...@douglas.co.ukDouglas
gt;
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Patrick Loll
pjl...@gmail.com
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to try.
The other thing I would suggest is to make a seedstock from those crystals
and add them to a random screen - you will almost certainly find new
conditions that avoid volatile precipitants.
See links below. I hope one of them works for you !
Good luck,
Patrick
___
. Meanwhile, the microscope keeps on truckin’; interesting to
reflect on the relative lifetimes of analog vs. digital tools…
Thanks in advance for any suggestions,
Pat
---
Patrick J. Loll, Ph. D. (he, him, his)
Professor
unications*, *70*(8), pp.1107-1115.
https://doi.org/10.1107/S2053230X14012552
More info
https://www.douglas.co.uk/mms.htm
Best wishes and good luck!
Patrick
___
Hi Kavya
1. Make a seed stock from the globules or anything else that you think
might be crystalline, and recreen.
data mining of the crystallization
conditions in a remark in the PDB. The concentrations that people reported
are below. There were eight reports where over 100 mg/mL was used. It
only goes up to 2004.
https://www.douglas.co.uk/PDB_data.htm
<https://www.douglas.co.uk/PDB_data.htm>
Go
protein was crystallized at slightly
higher protein concentrations, and slightly higher concentrations of
precipitant were used on average.
But it should be possible to make predictions. DeepMind is probably
working on this right now!
Best wishes,
Patrick
On Mon, Feb 5, 2024 at 3:06 PM kavyas
; Best,
> Jerome
>
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-------
Patrick J. Loll, Ph. D. (he, him, his)
Pr
e help!
Pat
---
Patrick J. Loll, Ph. D. (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philade
find a suitable resource.
Thanks in advance,
Pat
[This is me bowing to the fact that younger people appear to like to get their
information by watching videos, even though I much prefer to READ].
---
Patrick J
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> > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
> >
>
>
>
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> https://
other patents and patent applications.
Patents don't really apply to academics in practice.
Patents shouldn't be issued for things that are obvious
https://new.epo.org/en/legal/guidelines-epc/2023/g_vii_4.html
Patrick
On Fri, Jul 28, 2023 at 9:37 AM Randy John Read wrote:
> I
seems to
have been quiet for a while. Are people able to get their work done under OS
13? And have people encountered problems with any other structural biology
programs?
Cheers,
Pat
---
Patrick J. Loll, Ph. D
crushed crystals of your protein with the other ligand) -
so-called microseed matrix-screening.
https://doi.org/10.1107/S0907444907007652
Good luck
Patrick
On Sat, Feb 4, 2023 at 10:32 PM Mark J. van Raaij
wrote:
> PS it’s probably not a salt crystal…TCEP is not a salt, your ligand I
&
> >>
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> &
(and perhaps cheaper?) than connecting
the camera to software running on a PC.
Any thoughts/examples/tricks are welcome.
Thanks,
Pat
---
Patrick J. Loll, Ph. D. (he, him, his)
Professor of Biochemistry
the reactions are fast. Careful mixing
> (and adjusting the pH of the ADP beforehand) are important because the BeCl2
> stock will precipitate at neutral or elevated pH, and the BeFx solution is
> quite acidic.
>
>
>
-
/DiamondLightSource/durin/releases/tag/2019v1
and download the durin-plugin-macos.zip file
Unzip it and place the durin-plugin.so file in the directory of your
choice.
Cheers,
Pat Loll
> On 1 Jun 2022, at 4:08 AM, Kay Diederichs
> wrote:
>
> Hi Patrick,
>
&g
Loll
---
Patrick J. Loll, Ph. D. (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102 USA
(215) 762
...@douglas.co.ukDouglas Instruments Ltd.
Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
Directors: Patrick Shaw Stewart, Peter Baldock, Stefan Kolek
http://www.douglas.co.uk
Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
Regd. England 2177994, VAT Reg. GB 480
absurdly expensive); would anybody care to
recommend other options?
Much obliged for any suggestions (the more obsessive, the better).
Cheers,
Pat
---
Patrick J. Loll, Ph. D. (he, him, his)
Professor of
Phos-tag gels are an option (albeit a fiddly one).
Cheers,
Pat Loll
___
Patrick J. Loll, PhD (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St.
Philadelphia, PA 19102-
king supply - but also meets
> none of the stipulations.
>
-------
Patrick J. Loll, Ph. D. (he, him, his)
Professor of Biochemistry & Molecular Bio
eed-stocks. However it is
recommended that you keep crystals where the main precipitant was PEG
separate from crystals where the main precipitant was salt.
https://doi.org/10.1107/S2053230X14012552
https://doi.org/10.1107/S0907444907007652
or google MMS or rMMS.
Good luck, Patrick
On Tue, May
---
Patrick J. Loll, Ph. D. (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102 USA
(215) 762-7706
pjl...@gmail.co
was written (but
the intrinsic nature of the molecule hasn’t changed, so maybe not?).
Good luck.
Pat Loll
Patrick J. Loll, PhD (he,his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St.
Philadelphia, PA 1
Hi Saurabh
Of course you should use "rMMS" microseeding. See below
I hope it works !
Best wishes, Patrick
-- Forwarded message -----
From: Patrick Shaw Stewart
Date: Mon, Sep 9, 2019 at 10:12 AM
Subject: Re: [ccp4bb] Optimization from needle shaped crystals
To: David
in the paper my collaborator and I are now working on !
So probably not a good idea Jacob
Thx Patrick
On Thu, Feb 18, 2021 at 4:16 PM Jessica Bruhn
wrote:
> Hello,
>
> There have been some really excellent points raised by others (informed
> consent, feasibility, etc), but I would
eat it" -
that is, get as much of both A and B as possible - is to develop thermal
sensitivity. I.e. infect nose and throat but keep out of lungs and brain :
https://www.preprints.org/manuscript/202101.0389/v1
Thanks, Patrick
On Wed, Feb 17, 2021 at 9:46 PM Edwin Pozharski
wrote:
&g
-
> Many plausible ideas vanish
> at the presence of thought
> --
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quite large batches, but that product is
no longer available.
Thx Patrick
___
D'arcy A, Elmore C, Stihle M, Johnston JE. A novel approach to
crystallising proteins under oil. Journal of Crystal Growth. 1996 Oct
2;168(1-4):175-80.
https://www.sciencedirect.com/science/articl
b). However crystals of the same protein grown by cross-seeding
(with crystals of a homologous Fab) looked completely different and
diffracted to 2.3Å (figure 4c).
https://scripts.iucr.org/cgi-bin/paper?nj5193 (open access).
Your project shouts "seed me".
Hope it works
Patrick
O
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yet checked to see if
that will survive immersion in liquid nitrogen). Does anyone have any other
(better) ideas?
Much obliged in advance,
Pat
__
Patrick J. Loll, PhD
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102
reserved=0,
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, I mean the peaks of the histograms
(phenix.r_factor_statistics suggests R ~ 0.15-0.18, Rfree ~ 0.19-0.22)
I realize that I could probably dig up this information on my own, but I’m
(feeling lazy)/(desirous of the community’s wisdom).
Thanks,
Pat
Patrick Loll
pjl...@gmail.com
in the US, best wishes for a happy “Holy crap, even MORE
fireworks?!?!!” Day
Pat
---
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102
insights that might satisfy my curiosity and/or prevent future
mishaps of this sort.
Cheers,
Pat
__
Patrick J. Loll, PhD
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St.
Philadelphia
here any other obvious reason?
>
> Thank you,
> Maria
>
>
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ting to know whether the lung samples were less
temperature-sensitive than the throat ones, and whether this could explain
the observed divergent tropism - (which you also noted).
https://oldwivesandvirologists.blog/predicting-the-seasonality-of-covid/
Thx and stay warm (see my blog)
Patrick
On T
temperature-driven switch has been seen, switching between
translation (high temp) and replication (low temp). See the link below for
figures - described in words in my paper, below.
Best wishes
Patrick
Figures showing the "switch":
https://www.douglas.co.uk/f_ftp1/Seminar_by_Patrick_Sh
nt papers, are below.
Good luck to everyone and stay well,
Patrick
https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/
My paper in *Medical Hypotheses *
http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf
Narberhaus, Franz, Torsten Waldminghaus, and Sa
Instruments Ltd.
Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
Directors: Patrick Shaw Stewart, Peter Baldock, Stefan Kolek
http://www.douglas.co.uk
Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
Regd. England 2177994, VAT Reg. GB 480 7371 36
fication - or maybe it had broken down. Water was
running feely down the walls and poling on the floor, and the robot was
covered in condensation. Every non-stainless screw on the controller,
computer, robot etc was rusty. Interestingly, both the robot and the
computer still worked.
Patrick
O
ants don't have complex immune systems.
Could these multiple genes be a way to avoid being wiped out by disease?
Ie if the plant gets sick, it just switches on a batch of "reserve"
genes**. Is that possible?
Thx, Patrick
* This is a pet theory of mine: https://oldwivesandvi
on the
air-drop interface. Therefore you should dilute the protein and/or the
precipitant when you scale up.
Good luck, Patrick
http://scripts.iucr.org/cgi-bin/paper?S2053230X14015507
https://scripts.iucr.org/cgi-bin/paper?nj5193
On Mon, Sep 9, 2019 at 4:45 PM Claude Sauter
wrote:
> Le 09/09/2
j5193
Good luck, Patrick
On Sun, Sep 8, 2019 at 1:46 PM David Briggs
wrote:
> 4. Matrix microseeding. Make a seed stock from these crystals and then
> re-run your primary screens.
>
> https://www.ncbi.nlm.nih.gov/m/pubmed/25195878/
>
> --
> Dr David C. Briggs
> Senior
rd
to make sense of the results of a martingale.
Thx Patrick
PS Janet (Newman) do you have anything more up-to-date on this?
On Thu, Aug 1, 2019 at 10:24 AM Sergei Strelkov
wrote:
> Dear all,
>
>
> I wondered if someone could point me to a recent study on the importance
> o
atom of every residue on the surface of the proteins. I came up with . . .
hmm . . absolutely nothing useful.
I conclude that we need to start with regular screening for pretty much
every new sample that we have - so an unbiased empirical approach is the
only good way to go.
Thx Patrick
Galin
I take the view that I'm trying to communicate with as many people as
possible, without distracting them with my spelling . . . So go for US
spellings.
Sent from mobile
On Tue, 23 Jul 2019, 22:39 Goldman, Adrian,
wrote:
> ..and responding in the same vein:
>
> my OED says that its etymology als
are quite prone to breaking
down, which makes the queues (lines) to get onto them even longer.
That method might be (micro-scale) DLS – or something completely different.
Thx, Patrick
On Mon, Jul 15, 2019 at 8:44 PM Holton, James M <
270165b9f4cf-dmarc-requ...@jiscmail.ac.uk> wrote:
&
ds?) of labs all over the world - work that is largely wasted.
But it needs proper funding – and I don’t know how to get that.
Best wishes to all,
Patrick
Ps Of course I agree with Janet, Tom and others that good record-keeping is
essential. But there is a limit to what we will learn if
oltz-Gemeinschaft Deutscher Forschungszentren
> e.V.
>
> Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta
> Koch-Unterseher
> Geschäftsführung: Prof. Dr. Bernd Rech (Sprecher), Prof. Dr. Jan Lüning,
> Thomas Frederking
>
> Sitz Berlin, AG Charlo
Best regard
>
>
>
>
>
>
>
>
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---
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
ling however the surface can become contaminated with grease and
denatured protein. Either put them through a dishwasher (I've heard) or
rub them hard with something soft.
Thx, Patrick
On Thu, 31 Jan 2019 at 17:14, Goldman, Adrian
wrote:
> Yes, that was it! I just couldn’t rememb
t;
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---
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Mo
list, click the following link:
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-------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Drexel University College of Medic
Hi Careina
Expanding on what Tim says, try crushing your crystals to make a seed
stock, and adding it to a few *random screens - *preferably screens that
you have already tried with this target.
Search for instructions for MMS or rMMS online.
Good luck,
Patrick
On 14 August 2018 at 11:34
the oil and then diffuse into the drops. You
can take your time and harvest the crystals through the oil. The oil
protects the crystals, preventing evaporation of isopropanol.
Let me know if you (or anyone) would like some sample plates to try this
out.
See example and ref. bel
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---
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Drexel University College of Medi
s comparable to the
spreading doesn't mean that the crystals won't be ordered, and won't
diffract well.
Once I understood that I understood what I was seeing better when I checked
my drops.
Best wishes Patrick
On 5 July 2018 at 22:06, Sanishvili, Ruslan wrote:
> Hi Anirban,
&
*). I was disappointed that I only got one reviewer to support
my article by writing a report. But I felt that the format of the journal
would have been be very helpful for a controversial topic. Link below.
Patrick
__
*ResearchGate *https://en.wikipedia.org/wiki/ResearchGate#Crit
ences for reviewers and authors than the big commercial ones.
Pat
-------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Buildin
crystallization, or rMMS crystallization.
I hope it works - it very often does!
Good luck,
Patrick
On 4 June 2018 at 21:41, Janet Newman wrote:
> Liuqing Chen,
>
> Everything that has been said seems reasonable, but there are always
> infinite possibilities in crystallisation,
8
> 69120 Heidelberg
> Germany
> Phone: +49 6221 54 4796
> Email:
>
--
patr...@douglas.co.ukDouglas Instruments Ltd.
Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
Directors: Peter Baldock, Patri
angle of the light hitting the sample - I'm sure
others can explain better than I can.
Good luck, Patrick
On 7 March 2018 at 02:06, Chandramohan Kattamuri <
1c5b7cb6c764-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi
>
> I'm looking for suggestions on a good microscope for lo
r the help.
>
> -Rajesh
>
>
>
>
-------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu
That's very interesting. I guess it's an unusual manifestation of the
Hofmeister series.
It might give guidance to developers of screens for both crystallization
and cryoEM.
Thx, Patrick
On 9 January 2018 at 15:44, Andrew Mesecar wrote:
> Dear Jacob,
>
>
>
> One o
protein activity, could
> you patent such "binding site"? If not, how to make the best use of such
> findings?
>
>
> I would say that the best one can do with important novel
> data/information/knowledge/insights is to publish it so the world can
> benefit from it.
&
---
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
routine structure solution. But I always find it helpful to bear in mind,
as Frank suggests.
Very best wishes, Patrick
On 13 July 2017 at 14:49, Oganesyan, Vaheh wrote:
> What I’m about to write should be referred as a question rather than an
> answer. However, it might also help to fi
Gloria, would you be interested in used ones? I don't actually have any -
we threw them out a few months ago, I've just checked - but someone might
have some.
Best wishes, Patrick
On 11 July 2017 at 19:04, Gloria Borgstahl wrote:
> I have recently found out that these are no
rt of crystallization is to try lots of things without
thinking too much.
Patrick
On 12 July 2017 at 07:50, Vicky Tsirkone wrote:
> Dear Frank,
>
> I may see in the attached pic several nucleation points and a considerable
> amount of microcrystals. Based to my knowledge decreasing the c
Microseed them into two or three random screens.
Search for MMS and rMMS online.
Good luck
Patrick
On 10 July 2017 at 15:47, Liuqing Chen <519198...@163.com> wrote:
> hello everyone!
> I get a condition (10% w/v PEG 6000, 100mm HEPES PH7.0) in which my
> protein grow sma
ke an
advertisement.
I know very little about imaging systems, but I think you should at least
consider the systems made by Jansci, XtalQuest and XtalConcepts
There may be others.
Best wishes,
Patrick
On 30 June 2017 at 15:55, Chris Waddling wrote:
> We had the Tritek CrystalPro and now
n
DNA crystals?
Patrick
On 19 June 2017 at 15:20, Joseph Ho wrote:
> Dear all:
>
> I would like to seek your opinion on our crystal hits. We are working
> on protein/dsDNA complex. By changing different protein and DNA
> (14-22bp) constructs, we recently got some hits from commer
?
Thanks as always,
Pat
---
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop
Hena
There was a very interesting paper by Peter Sun and coworker from 2002.
They pointed out that there is a very strong bias towards crystallizing
protein-protein complexes with PEG rather than salt as the main precipitant.
Patrick
___
Radaev and Sun
I’m looking at my copy of Terrance Cooper’s ‘The Tools of Biochemistry’ (Wiley,
1977). It identifies two approaches to fractionating gradients. The first is
the one Michael describes (allowing the liquid to drip out of the bottom). The
other is to pierce the bottom of the tube, and then pump a v
get some results, so we’d like to farm
it out rather than get the technology going in-house). Can anyone recommend a
group (ideally in the US, for logistical ease)?
Thanks for any help.
Cheers,
Pat
---
Patrick
Yes, but the kids will want to know WHY there is an energy barrier.
I prefer my explanation below.
Happy New Year to all
Patrick
_
> I am especially needing help with the concept of nucleation, and why
nucleation is slower and then crystal growth faster once nuclei h
Sadly, I have seen numerous examples of reasonably-sized crystals that give no
observable ordered diffraction (I shot a few this weekend, in fact). I can’t
give you evidence for what is happening, but I guess that you can build a
macroscopic assembly using lattice interactions that are only mode
Ave atque vale.
The EDS was hugely useful (and will continue to be so in its new manifestation,
we hope)—thanks to everyone who made it happen!
Pat
> On 13 Dec 2016, at 12:51 PM, Gerard DVD Kleywegt
> wrote:
>
> Hi all,
>
> After tirelessly serving the scientific community with (mostly)
stock.
In practice 100% PEG 600 worked for 5 of the 6 model proteins that we
looked at. The remaining seedstock worked with seed crystals suspended in
4M amm. sulfate.
I hope it works for you.
Best wishes, Patrick
___
Ref for stabilizing seed stocks with va
; Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij
-
lists from library websites for example.
Philip
On Fri, Jun 19, 2015 at 5:55 AM, Jann-Patrick Pelz <
jann.p...@biozentrum.uni-wuerzburg.de> wrote:
Dear all,
we are currently preparing a manuscript for publication in Acta Cryst. D.
Neither the Output Style delivered with Endnote X7 nor the Outs
other Settings lead to the same wrong abbreviations.
Did someone encounter the same problems and did you maybe find a solution?
Best regards,
Jann
Jann-Patrick Pelz
Lehrstuhl für Biochemie
Biozentrum - Am Hubland
97074 Würzburg
0931-31 83334
jann.p...@uni-wuerzburg.de
mple plates to try.
Best wishes,
Patrick
On 12 June 2015 at 22:11, Thomas, Leonard M. wrote:
> Hi All,
>
> We have gotten some very nicely formed crystals out of a couple of
> different volatile solvents recently. Besides looking for something easier
> to work in does anybody
inary transmission mode can
both work well - good to have both if possible.
Good luck,
Patrick
On 27 March 2015 at 13:08, Ronnie Berntsson wrote:
> Dear all,
>
> I’m currently looking in to buying a new microscope for viewing crystal
> plates, mounting crystals etc, and would love som
t.
I agree that Al's Oil (silicone) should be avoided from this point of view
- although I would certainly use it anyway for screening experiments
(whether aerobic or anaerobic).
Riveting stuff.
Thx to all, Patrick
On 18 March 2015 at 18:58, Tristan Croll wrote:
> It's a little comp
robic) microbatch produces far superior crystals
to V.D. for no obvious reason - it's well worth trying for both screening
and optimization.
Best wishes
Patrick
On 11 March 2015 at 10:17,
wrote:
> Dear CCP4BBer's
>
> Apologies for the off-topic post, but the CCP4BB seems to be the b
ou very much in advance,
>
> Francesca
>
>
--
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Hi Tim,
Thank you for the clarification.
Is there a way to extract from the PDB all the CCP4/Phenix structures then?
From your answer I take it there is no way?
Patrick
> -Original Message-
> From: t...@shelx.uni-ac.gwdg.de
> Sent: Sat, 24 Jan 2015 20:35:54 +0100
>
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