Indeed! Scientists in the Soviet Bloc got paid for publishing their scientific
papers (and maybe for citations as well - not sure about that one)! We need to
change the current system! Although these changes could be accompanied by many
other pleasant virtues of the Soviet regime.
Petr
> On
Petr Leiman
University of Texas Medical Branch
Department of BMB
Basic Sciences Building 6.600D
301 University Blvd
Galveston, TX 77555-0647
Cell: 832 908 6635
Office: 409 747 2078
https://scsb.utmb.edu/faculty/Leiman.asp
> On Dec 16, 2017, at 4:42 PM, Anastassis Perrakis wr
If your signal goes all the way to the half Nyquist frequency, oversample your
map to have the pixel size equal to 1/3rd of the highest resolution. Your map
will look much better in coot. Real space fitting will work much better as
well.
Best,
Petr
> On May 17, 2017, at 11:24 AM, MyeongSeon
A small erratum is needed unfortunately. The sequence identity of 4UHV to 2P5Z
is 19% (but not the exceptional 15% as I wrote originally). Nevertheless,
Phaser successfully finding a solution for a 19% SI model is no small feat.
> On Mar 16, 2016, at 09:48, Petr Leiman wrote:
>
>
quot;.
On 03/12/2015 08:49 PM, Petr Leiman wrote:
> Dear Community,
>
> What is the reason of placing the CCP4 PATH and other path-related variables
> in front of existing variables? This forces a linux system to use
> CCP4-distributed wish in all applications by default. Note
caused by CCP4 wish.
Would it be possible to append CCP4 path variables by default instead of rather
rudely jumping in front of the queue?
Thank you,
Petr
--
Petr Leiman
EPFL
BSP 415
CH-1015 Lausanne
Switzerland
Office: +41 21 69 30 441
Mobile: +41 79 538 7647
Fax: +41 21 69 30 422
://pva.scripps.edu/program.html
The all-inclusive registration fee is rather modest considering that the site
is a 4-star resort hotel and all talks will take place in a large congress hall.
Hope to see you in Les Diablerets!
Sincerely,
Petr Leiman
--
Petr Leiman
Laboratory of Structural Biology
On Apr 24, 2014, at 11:39, Petr Leiman
mailto:petr.lei...@epfl.ch>> wrote:
Dear All,
We are looking for an explanation for a very strange observation.
Problem:
We have two fully independent data sets (two different crystals), in which the
Bijvoet Difference Fourier map peak of one part
much,
Petr
--
Petr Leiman
EPFL
BSP 415
CH-1015 Lausanne
Switzerland
Office: +41 21 69 30 441
Mobile: +41 79 538 7647
Fax: +41 21 69 30 422
how diffraction is recorded
by the detectors we use today and we can simply ignore it.
Petr
Petr Leiman
EPFL
Switzerland
On 04/02/2014 04:39 AM, Edward A. Berry wrote:
> Encouraged by recent help from the BB in filling in gaps in my
> understanding, maybe I can get help
> diffraction experiment on a "small molecule" crystal. One good reason
>>>>
>>>>> for using Si(111) is because Si(222) is a systematic absence, so you
>>>>
>>>>> don't have to worry about the lambda/2 x-rays going down the pipe at
>>>>
>>>>> the same angle as the "lambda" you selected. However, Si(333) is not
>>>>
>>>>> absent, and unfortunately also corresponds to the 3rd peak in the
>>>>
>>>>> emission spectrum of an undulator set to have the fundamental coincide
>>>>
>>>>> with the Si(111)-reflected wavelength. This is probably why the
>>>>
>>>>> "third harmonic" is often the term used to describe the reflection
>>>>
>>>>> from Si(333), even for beamlines that don't have an undulator. But,
>>>>
>>>>> technically, Si(333) is n
>>>>
>>>> ot a "har
>>>>
>>>> monic" of Si(111). They are different reciprocal lattice points and each
>>>> has its own structure factor. It is only the
>>>> undulator that has "harmonics".
>>>>
>>>>>
>>>>
>>>>> However, after the monochromator you generally don't worry too much
>>>> about the n=2 situation for:
>>>>
>>>>> n*lambda = 2*d*sin(theta)
>>>>
>>>>> because there just aren't any photons at that wavelength. Hope that
>>>> makes sense.
>>>>
>>>>>
>>>>
>>>>> -James Holton
>>>>
>>>>> MAD Scientist
>>>>
>>>>>
>>>>
>>>>>
>>>>
>>>>> On 8/20/2013 7:36 AM, Pietro Roversi wrote:
>>>>
>>>>>> Dear all,
>>>>
>>>>>>
>>>>
>>>>>> I am shocked by my own ignorance, and you feel free to do the same,
>>>>
>>>>>> but do you agree with me that according to Bragg's Law a diffraction
>>>>
>>>>>> maximum at an angle theta has contributions to its intensity from
>>>>
>>>>>> planes at a spacing d for order 1, planes of spacing 2*d for order
>>>>
>>>>>> n=2, etc. etc.?
>>>>
>>>>>>
>>>>
>>>>>> In other words as the diffraction angle is a function of n/d:
>>>>
>>>>>>
>>>>
>>>>>> theta=arcsin(lambda/2 * n/d)
>>>>
>>>>>>
>>>>
>>>>>> several indices are associated with diffraction at the same angle?
>>>>
>>>>>>
>>>>
>>>>>> (I guess one could also prove the same result by a number of Ewald
>>>>
>>>>>> constructions using Ewald spheres of radius (1/n*lambda with n=1,2,3
>>>>
>>>>>> ...)
>>>>
>>>>>>
>>>>
>>>>>> All textbooks I know on the argument neglect to mention this and in
>>>>
>>>>>> fact only n=1 is ever considered.
>>>>
>>>>>>
>>>>
>>>>>> Does anybody know a book where this trivial issue is discussed?
>>>>
>>>>>>
>>>>
>>>>>> Thanks!
>>>>
>>>>>>
>>>>
>>>>>> Ciao
>>>>
>>>>>>
>>>>
>>>>>> Pietro
>>>>
>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>
>>>>
>>>>>> Sent from my Desktop
>>>>
>>>>>>
>>>>
>>>>>> Dr. Pietro Roversi
>>>>
>>>>>> Oxford University Biochemistry Department - Glycobiology Division
>>>>
>>>>>> South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339
>>>>
>>>>>
>>>>
> >
--
Petr Leiman
EPFL
BSP 415
CH-1015 Lausanne
Switzerand
Office: +41 21 69 30 441
Mobile: +41 79 538 7647
Fax: +41 21 69 30 422
, but maybe they have been
> suffering in silence! Could you let us know why you find this feature
> extremely useful?
>
> Best wishes,
>
> Randy Read
>
> On 2 Jul 2013, at 18:41, Petr Leiman wrote:
>
>> I have just found out that phaser v. 2.5.2 in ccp4 6.3.0-
has not been discovered and fixed already. If there
is a reason to this new output column behavior, it would be very useful
to hear this reason.
Sincerely,
Petr
--
Petr Leiman
EPFL
BSP 415
CH-1015 Lausanne
Switzerand
Office: +41 21 69 30 441
Mobile: +41 79 538 7647
Fax: +41 21 69 30 422
.html
Best wishes,
Petr
--
Petr Leiman
EPFL
BSP 415
CH-1015 Lausanne
Switzerland
Office: +41 21 69 30 441
Mobile: +41 79 538 7647
Fax: +41 21 69 30 422
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>]
on behalf of Jason Vertr
and additional information please contact Prof. Petr Leiman
(petr.lei...@epfl.ch<mailto:petr.lei...@epfl.ch>)
---
Petr Leiman
EPFL
BSP 415
CH-1015 Lausanne
Switzerland
Office: +41 21 69 30 441
Mobile: +41 79 538 7647
Fax: +41 21 69 30 422
Since this is now public domain knowledge and if this gets ever published, Phil
has my vote to be the first author!
Petr
On Mar 27, 2013, at 6:09 PM, Phil Jeffrey wrote:
> That's quite brave - shipping your entire structure to people that could be
> actual competitors. But it was fun to play
block emails with 1+MB attachments?
Thank you,
Petr
Prof. Petr Leiman
EPFL
BSP-415
CH-1015 Lausanne
Switzerland
On Mar 27, 2013, at 5:22 PM, Tom Van den Bergh wrote:
Dear members of ccp4bb,
I need some help with the refinement of my structure of a variant of mRFP
or CCP4BB.
Thank you,
Petr
On Nov 22, 2012, at 3:04 PM, Petr Leiman wrote:
> Dear all,
>
> Hgen GUI does not start (the error message is below). The CCP4 version is
> 6.3.0-009 (64 bit). The system is 2.6.35-32-generic #67-Ubuntu SMP x86_64
> GNU/Linux. Is this uniqu
Dear all,
Hgen GUI does not start (the error message is below). The CCP4 version is
6.3.0-009 (64 bit). The system is 2.6.35-32-generic #67-Ubuntu SMP x86_64
GNU/Linux. Is this unique to our system configuration?
Thank you.
Petr
The error message is:
can't use non-numeric string as operand
with a
> lot of new features (mainly for small molecules) and no known bugs, so I hope
> to release it soon. If anyone would like to try it now please send me an
> email.
>
> George
>
> On 11/19/2012 02:13 PM, Petr Leiman wrote:
>> Dear Developers of Coot,
>>
>
the future.
Thank you,
Petr
Petr Leiman
EPFL
BSP-415
CH-1015 Lausanne
Switzerland
ite.
Petr
On Jun 20, 2012, at 12:38 AM, Jacob Keller wrote:
> Is part of your question based there being many ways to superimpose
> structures, which there are?
>
> JPK
>
> On Tue, Jun 19, 2012 at 5:34 PM, Petr Leiman wrote:
>> Would anyone be kind enough to explain
dentical, one HAS to superimpose them, i.e. to move
all (or selected) atoms to be as close in space as possible and only then
calculate the RMSD for the superimposed or all atoms.
Thank you in advance,
Petr
----
Petr Leiman
EPFL
BPS-415
CH-1015 Lausanne
Suisse
On Jun 19, 2012, at 5:0
Jacob, do not worry. Data collection for a typical crystal takes only 0.75
seconds.
Petr
On May 9, 2012, at 5:18 PM, Jacob Keller wrote:
I saw something online about the EIGER 16M: 201 GB of data per second! Is that
number correct?
JPK
On Wed, May 9, 2012 at 9:58 AM, Meitian Wang
mailto:me
presence of high NCS does not guarantee a success even if your initial
model is "good" as described in Section 9 here:
http://www.ncbi.nlm.nih.gov/pubmed/11526317
Petr
--
Petr Leiman
EPFL
IPSB-LBBS
BSP-415
CH-1015 Lausanne
Suisse
le, I am sorry you are likely to receive this message twice...
> Dale Tronrud
>
> On 1/19/2012 12:51 PM, Petr Leiman wrote:
>> It would be so much more convenient to call these techniques (MAD, SAD,
>> etc.) by their inventor's name. This would simplify things
It would be so much more convenient to call these techniques (MAD, SAD, etc.)
by their inventor's name. This would simplify things immensely simultaneously
eliminating CCP4BB MADisagreements.
Although in our days of copyrights wars, the journals and perhaps conferences
where these methods were
Dear Tim,
I agree with you completely. The question then becomes why does the automatic
weighting scheme in refmac allow R and R-free to run away from each other by 8%
in a 1.1 A resolution structure?
Petr
On Dec 8, 2011, at 6:50 PM, Tim Gruene wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Ha
For the second time today I have to apologize. In no way I wanted to discourage
anyone and especially people new to crystallography from posting questions to
this BB. Especially good thoughtful questions.
Sincerely,
Petr
On Dec 8, 2011, at 5:24 PM, Petr Leiman wrote:
> wrote:
>>
wrote:
> I am not sure that sending links is the way to go. Our company blocks many
> websites that it considers not of professionel interest and were employees
> may spend too much time.
What a brilliant idea! If only this could be implemented in academia. Our Ph.D.
students would stop aski
Coot is beyond competition (is there any nowadays?), but it cannot do what Yuri
Pompeu asked about.
Petr
On Dec 8, 2011, at 10:10 AM, Francois Berenger wrote:
> On 12/08/2011 05:11 PM, Petr Leiman wrote:
>> Dear Bostjan,
>>
>> There is Chimera for almost anything you c
Do I feel stupid! My previous message about Chimera should have been addresses
to Yuri Pompeu, but not to Bostjan Kobe.
Sincerely,
Petr
On Dec 8, 2011, at 6:26 AM, Yuri Pompeu wrote:
> I once saw a figure showing the protein as surface, but instead of having it
> coloured by atom type
> or p
Dear Bostjan,
There is Chimera for almost anything you can think of. Search for
"Structure-Based Sequence Alignment" on this page:
http://www.cgl.ucsf.edu/chimera/features.html
Petr
On Dec 8, 2011, at 6:39 AM, Bostjan Kobe wrote:
> Consurf will do this for you.
>
> Bostjan
>
> ---
> Bostja
That lmgtfy.com is as almost as cool as HHpred.
Thanks for a very useful piece of information!
Petr
On Nov 3, 2011, at 2:06 PM, Tim Gruene wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Zhang Qi,
>
> I like this url: http://www.lmgtfy.com/?q=topology+diagram+protein
> whi
a new run it stopped in the middle of TF. The
remedy is to explicitly lower the resolution of the input data (that was a 1.2
A resolution data with a smallish unit cell).
I can provide the log files and the mtz file if necessary.
Sincerely,
Petr
---
Petr Leiman
EPFL
IPSB-LBB
Dear all,
What is the status of Denzo/HKL2000 availability/support for the Pilatus 6M
detector?
Thank you,
Petr
Apologies for suggesting a non-CCP4 solution, but UCSF Chimera can do that and
more (interactively!):
Tools -> Higher Order Structure -> Unit cell
Petr
On Jun 30, 2011, at 2:52 PM, Hargreaves, David wrote:
>
> Does anyone have a rigorous method (or script) for generating an extended
> latti
Totally support the statements below. We have had several proteins with A280
absorbance of 0.1 or less (at 1 mg/ml). You _have_ to use Bradford in the
Nanodrop or whatnot to measure the concentration.
Before purchasing the Nanodrop we used a Hellma TrayCell and a "normal" UV/Vis
instrument. Sim
No offense intended, but NMR is not a structure determination method. One
_estimates_ what a structure _might_ look like if such and such
"restrainoconstraints" applied. We always speak of how undetermined our
crystallographic data are, how poor of an estimate is our R/R-free. Shall we
even dis
lectrons
>> in perhaps a rather divergent beam?
>> Shall we discuss off line (with Jacob) and present our conclusions
>> when/if we get agreement?
>> Regards
>> Colin
>>
>>
>>
>>> -Original Message-
>>> From: C
act journal would probably upset
> my physicist colleagues - that's fine though!
>
> Regards
> Colin
>
>> -----Original Message-
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>> Petr Leiman
>> Sent: 14 April 2011 21:07
>
>> -Original Message-
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>> Petr Leiman
>> Sent: 14 April 2011 16:23
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Femtosecond Electron Beam
>>
>> People are looking into how t
People are looking into how to fit the old retired MeV microscopes with pulsed
electron guns (problem is there are very few of those beasts left). If this
works, such a machine will produce equivalent results to FEL but at a fraction
of the cost.
The group at Eindhoven, which Colin had mention
Hi Mark,
What about UCSF Chimera? Very easy to use.
http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html
More on the topic:
http://www.cgl.ucsf.edu/chimera/animations/animations.html
Check out the "Nuclear pores" movie. Amazing stuff. A few years back one had to
pay huge $$$ for M
Another vote for Ubuntu.
I have to say that a Live CD version is not a good test of this excellent Linux
distro. We have 3 identical PCs. On two of these the latest version of 10.10
64bit live cd loads to a blank (completely black) screen. Google: "blank screen
ubuntu live cd" - thankfully ther
osts 50-65 CHF per
day.
The registration deadline:
October 31, 2009
http://ipsb.epfl.ch/page82078.html
Sincerely,
Petr
-
Petr Leiman
Head of the Laboratory of Structural Biology and Biophysics
I
worse than an older generation Nikon instrument (halogen lamp)
with an objective of a smaller aperture.
Petr
-
Petr Leiman
École Polytechnique Fédérale de Lausanne (EPFL)
Cubotron/BSP-415
CH-1015 Lausanne
Switzerland
- Original Message -
From: &qu
Hello all,
While testing a newly installed ARP/wARP interface (ver. 7.0.1) in ccp4i
(ver. 6.1.0) on Ubuntu (8.10) I noticed that the Fobs and Sigma pull-down
menus are missing from the ARP/wARP Quick Fold window. This is accompanied
by the following error message, which is output in stderr by
A post-doctoral position is available (in the department of Biological
Sciences, Purdue University, Indiana 47907, USA) for structural studies of
viruses and their interaction with host cells. Applicants should have
experience in virus or protein crystallography and in molecular biology.
Experi
ology, biophysics or biochemistry
are encouraged to apply.
The positions are available starting October 1st, 2008.
Applicants are invited to send a CV and a letter of motivation describing
research experience, interests and key accomplishments, and contact
information of two to four referees to Dr.
On behalf of Michael Rossmann:
A post-doctoral position is available in a virus structure laboratory.
Applicants should have experience in computer program development or
adaptation for crystallography or electron microscopy. Please e-mail
applications to Michael Rossmann, [EMAIL PROTECTED] (D
yes you are right, but I assumed if people see a cloud of condensed
fog over their LN2 bath they should remove that by
a) filling up the bowl completely e.g. some LN2 drips out of the bowl
b) blow the fog away before you dip
I think the original poster meant the relatively low heat conduction of
Dear Raja,
Do you seriously believe that you will find help on this board after making
us all download your 2 * 4.1 MB of crap NOT RELATED TO CCP4???
Good luck in your future endeavors!
Petr
- Original Message -
From: "Raja Dey" <[EMAIL PROTECTED]>
To:
Sent: Thursday, April 10,
- Original Message -
From: "Jenny Martin" <[EMAIL PROTECTED]>
To:
Sent: Thursday, August 23, 2007 5:46 PM
Subject: Re: [ccp4bb] The importance of USING our validation tools
My question is, how could crystals with 80% or more solvent diffract so
well? The best of the three is 1.9A reso
ER SUSPECT STRUCTURES from the same group or same authors
published elsewhere???
Petr Leiman
Dept. of Biological Sciences
Purdue University
West Lafayette, IN
I just found this old thread in my CCP4 folder.
1. mencoder can convert pymol's quicktime format movies into avi movies.
2. Powerpoint movie handling is beyond ancient and sometimes AVI movies can be
played in MS mediaplayer but Powerpoint would not play them. The remedy is to
use "good"-sized fra
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