Re: [ccp4bb] Updating Ubuntu 18 LTS to 20?

[Jim Fairman]

Hi Domen,

I have been running 20.04 for quite some time now without any issues.  In
my experience, performing in-place upgrades from a previous version (eg:
14.04 to 16.04, 16.04 to 18.04) caused some issues and I usually ended up
having to wipe the system and perform fresh installs, but your mileage may
vary.  My standard operating procedure is to backup your home directory and
any important files and perform a fresh install.

The rolling release distributions like Arch and Manjaro avoid the issues of
having to perform upgrades across major versions, but always running the
"latest" packages may sometimes cause issues.  However, I haven't found
this in my usage of them over the past 4 or 5 years.

Cheers, Jim
------
Jim Fairman
C: 1-240-479-6575


On Fri, Jan 14, 2022 at 1:00 PM Domen Zafred  wrote:

> Hi all,
>
> has anyone updated the Ubuntu 18.04 LTS Bionic Beaver to the never 20.04?
> That means with programs we usually have installed (java, phython, xds,
> ccp4 & coot, phenix, R, data warrior, pymol, nomacine, etc)? Any troubles,
> recommendations?
> 22 LTS is coming out this year, I'm not sure if jumping from 18 to 22
> would be a good idea, but 18 is getting old.
>
> Thanks for any hints
>
> Domen
>
> --
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Re: [ccp4bb] Structural Alignment

[Jim Fairman]

I used STRAP back in the late 2000s to do structure-based sequence
alignments of some TonB Dependent transporters:
http://www.bioinformatics.org/strap/

Looks like it is still being updated.

Cheers, Jim
--
Jim Fairman
C: 1-240-479-6575


On Wed, Apr 8, 2020 at 10:22 AM Guillaume Gaullier 
wrote:

> Hi Armando,
>
> This seems doable with ChimeraX: https://www.cgl.ucsf.edu/chimerax/
>
> More specifically, its matchmaker command will align two structures and
> print the corresponding sequence alignment:
> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
> You can then save the sequence alignment to a file, and use it in your
> favorite sequence alignment program along with the sequences for which you
> don’t have a structure.
>
> This is one option among many, as pretty much every structure
> visualization program can superimpose two similar structures (but I don’t
> know how many of them make it as easy to save the sequence alignment).
>
> Hope this helps,
>
> Guillaume
>
>
> On 8 Apr 2020, at 19:04, Armando Albert  wrote:
>
> Dear all,
> I want to align two structures and then, I want to align several sequences
> to that structural alignment.
> How can I do this?
> Armando
>
> 
>
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>
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Re: [ccp4bb] Clear Linux

[Jim Fairman]

David,

Luckily, phoronix has also benchmarked 10 different linux OSes on a Ryzen 7
1800X and a Threadripper 1950X chip:
https://www.phoronix.com/scan.php?page=article=ryzen-linux-10way=3

--
Jim Fairman
C: 1-240-479-6575


On Thu, Feb 7, 2019 at 8:16 AM David Schuller  wrote:

> I would be wary of an OS developed and promoted by a hardware
> manufacturer (Intel). The Phoronix benchmarks you linked were conducted
> on an Intel Xeon chip. I wonder how Clear OS performs with AMD chips,
> which are featuring very attractive performance and price recently.
>
>
>
> On 2/7/19 10:38 AM, Karthik Paithankar wrote:
> > Dear Program devs and enthusiasts,
> >
> > After seeing James' email (on dismal CPU performance), I was searching
> > for various ideas and found the so-called "Clear Linux Project". Seems
> > " function multi-version patch" leads to significant improvements.
> > Though I could install the precompiled binary of CCP4 and phenix
> > without any issues but there are no improvements to runtime as FMV
> > needs 'patching' and compiling.
> >
> > Could DIALS, CCP4 or Phenix programmers see if this is
> > useful/possible? Has anyone tried it?
> >
> > https://clearlinux.org/documentation/clear-linux/tutorials/fmv
> >
> https://www.phoronix.com/scan.php?page=article=clear-faster-blas=1
> >
> > Best regards,
> > Karthik Paithankar
> >
> >
> >
> > On 30/11/2018, James Holton < > wrote:
> >> I have a dissenting opinion about computers "moving on a bit".  At least
> >> when it comes to most crystallography software.
> >>
> >> Back in the late 20th century I defined some benchmarks for common
> >> crystallographic programs with the aim of deciding which hardware to
> >> buy.  By about 2003 the champion of my refmac benchmark
> >> (https://bl831.als.lbl.gov/~jamesh/benchmarks/index.html#refmac) was
> the
> >> new (at the time) AMD "Opteron" at 1.4 GHz.  That ran in 74 seconds.
> >>
> >> Last year, I bought a rather expensive 4-socket Intel Xeon E7-8870 v3
> >> (turbos to 3.0 GHz), which is the current champion of my XDS benchmark.
> >> The same old refmac benchmark on this new machine, however, runs in 68.6
> >> seconds.  Only a smidge faster than that old Opteron (which I threw away
> >> years ago).
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
> --
> ===
> All Things Serve the Beam
> ===
> David J. Schuller
> modern man in a post-modern world
> MacCHESS, Cornell University
> schul...@cornell.edu
>
> 
>
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Re: [ccp4bb] 3D stereo and pymol

[Jim Fairman]

I had a Windows 7 machine that would run Quad buffered stereo back around
2009, haven't had a chance to try with Windows 10.

On Wed, Jan 30, 2019, 02:03 Jan Stransky 
wrote:

> Dear all,
>
> I started looking into the never ending story of stereo in
> crystallography... As with our standardized linux setup we probably are not
> willing to move to X.org-world, if was wondering, if anybody was succesful
> to make stereo working in Windows 10. I did read some NVIDIA forum, and it
> seems that 3d vision is not very supported by NVIDIA, even for gamers...
> Was anybody able to mke it work with Geforce cards, to save few bucks?
>
> Best regards,
>
> Jan
> Dne 03.01.2018 v 10:42 Wim Burmeister napsal(a):
>
> I answer a bit late, but I repost a message on 3D graphics from Mai 2017 :
>
> Hello,
>
> we just wanted to share our experience in finding a configuration which
> allows to use 3D graphics under linux using Nvidia GeForce 3D glasses.
>
> We had quite a hard time to find a configurations which works correctly.
>
> We finally used Debian linux with a xfce desktop. Other recent desktops
> use a tiling which is not compatible with 3D graphics.
>
> The hardware consists of
>
>- a DELL Precision T5810  desktop computer with an Nvidia Quadro M4000
>(8 Gbyte memory, 4 DP) graphics card
>- Nvidia GeForce 3D Vision 2 (NVIDIA GEF 3D VISION 2 GLASSES KIT)
>active stereo glasses
>- a stereo connector PNY Quadro 4000 3D for the synchronization of
>graphics card and glasses
>- an ASUS 24" LED 3D - VG248QE display
>- a DisplayPort-DisplayPort cable
>
> The Nvidia linux drivers from version 367.57 can handle the current
> version of the Nvidia glasses.
>
> For an obscure reason a direct DP-DP connection between graphics card and
> display is absolutely required in order to obtain fully working stereo. If
> a DP-DVI dual link adapter is used, the stereo does not work on the top and
> the bottom part of the screen. This is true for a native DELL active
> adaptor or generic models. The exact reason remains unresolved, but the
> solution is to use a direct DP-DP connection. This limits the available
> choice of displays which require 120 Hz for 1080*1980 screen resolution and
> a DP input. We have been choosing a “Nvidia 3D ready” model.
>
> There has been a considerate about of exchange about this problem on
>
>
> https://devtalk.nvidia.com/default/topic/992892/linux/partially-working-stereoscopic-effect-with-3d-vision-under-debian-linux/
>
> The setup comes with a price tag of about 1600 € free of taxes.
>
> coot, pymol and chimera work straight without problems in hardware stereo
> mode. The experience is absolutely great.
>
> Best
>
> Wim
> --
>
> Wim Burmeister
> Professeur
> Institut de Biologie Structurale (IBS) CIBB
> 71 avenue des Martyrs
> CS 20192
> 38044 Grenoble Cedex 9, FRANCE
> E-mail: wim.burmeis...@ibs.fr
> Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
> website
> 
>
>
>
> --
>
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Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

[Jim Fairman]

The newest version of KDE Neon works.  You just have to turn compositing
off.
--
Jim Fairman
C: 1-240-479-6575


On Thu, Dec 20, 2018 at 2:33 PM Guenter Fritz <
guenter.fritz.phenix.c...@gmail.com> wrote:

> Dear Adarsh,
>
> just an add-on to the instructions of the others. Since GNOME is not
> anymore compatible with stereo, we use successfully Xubuntu (18.04) with
> NVIDIA drivers.
> Best , Guenter
> > Hello everyone
> >
> > We have just purchased a Dell workstation for crystallography data
> analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but
> failed to do so. Please help me out with this one. Some relevant
> information is as follows:
> > OS: Ubuntu 16.04 LTS
> > Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
> > Monitor: Asus VG248QE
> >
> > Thanks and regards
> > Adarsh Kumar
> > Suo Lab
> > Florida State University College of Medicine
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
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>
> 
>
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Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

[Jim Fairman]

If you want to use it with linux, the 3-pin connector is required.  You can
buy a cable that plugs into an output on the video card and then provides
an "Nvidia 3D Stereo Bracket" 3-pin adapter to plug the little pyramid into.

Here is a link to Dell's site, but you can get it elsewhere as well:
http://accessories.dell.com/sna/productdetail.aspx?c=us=en=fed=16=A7035595

I can vouch for the VG248QE monitors working with 3D Vision 2, I have 2 of
them.

Cheers, Jim
------
Jim Fairman
C: 1-240-479-6575


On Thu, Dec 20, 2018 at 12:46 PM Adarsh Kumar 
wrote:

> Hello everyone
>
> We have just purchased a Dell workstation for crystallography data
> analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but
> failed to do so. Please help me out with this one. Some relevant
> information is as follows:
> OS: Ubuntu 16.04 LTS
> Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
> Monitor: Asus VG248QE
>
> Thanks and regards
> Adarsh Kumar
> Suo Lab
> Florida State University College of Medicine
>
> 
>
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Re: [ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

[Jim Fairman]

Daniel,

To best of my knowledge, options for 3d stereo on Mac are limited to
Zalman:
https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Zalman_Stereo

If you're willing to go to Linux or Windows, you can do an Nvidia Quadro
Card with a 120 or 144Hz monitor with a 3D Vision glasses kit.

Cheers, Jim

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Jim Fairman
Principal Scientist II
Roche Sequencing Solutions
2841 Scott Blvd
Santa Clara, CA 95050
fairman@gmail.com jim.fair...@roche.com




--
Jim Fairman
C: 1-240-479-6575

On Fri, Mar 2, 2018 at 8:24 AM, Daniel M. Himmel, Ph. D. <
danielmhim...@gmail.com> wrote:

> I'm looking for some computer hardware advice.
> I have a MacBook Pro with a "Retina" screen and
> an Intel HD Graphics 4000 1536 MB graphics card,
> running OS X 10.11.16 ("El Capitan"), and I would
> like to view structures in 3-D in Coot.
>
> Which computer monitors and which 3-D glasses brands
> would allow me to view 3-D graphics in Coot?  Should I
> be going for dynamic 3-D glasses?
>
> -Daniel
>
>

Re: [ccp4bb] 3D stereo and pymol

[Jim Fairman]

Reporting in a setup that we just made: Quadro P4000 + 3 pin stereo bracket
+ 3d vision 2 kit + ASUS VG248QE.

Running System76's PoPOS Ubuntu 17.10 distro - you'll have to install a
desktop environment that supports non-compositing (ie: XFCE).

Works beautifully.



--
Jim Fairman
C: 1-240-479-6575

On Tue, Nov 28, 2017 at 6:40 AM, mesters <mest...@biochem.uni-luebeck.de>
wrote:

> Hi,
>
> yes, consumer cards do have OpenGL implemented on a chip but the Nvidia
> driver did not allow OpenGL 3D to work until February 2013. As of Nvidia
> driver version 314.07, Nvidia added OpenGL quad buffered 3D Stereo for
> GeForce cards (at least under MS Windows 7/8). However, this was never
> officially announced and officially supported and only works if the monitor
> is preset to run at 120 Hz and the software automatically switches into
> full-screen mode. Sadly, windowed applications will not work. Under MS
> Windows 10, it does not seem to work anymore.
>
> We have a monitor with a build in emitter and that one works with the
> smaller/cheaper Quadro cards without the 3-pin connector but, it is
> virtually impossible nowadays to get such a monitor in order to avoid
> needing to buy an expensive Nvidia card with a 3-pin connector.
>
> To enjoy OpenGL quad buffered 3D Stereo, you will at least need a Quadro
> K4000/P4000/4000 with separate 3-pin bracket (all-in-all very expensive
> solution) or you will need to buy an older FX model such as the FX3700 with
> build-in 3-pin connector.
>
> At the Bay in the USA, unused / brand-new FX3700s are being offered right
> now for about 90-110 US$. That's the cheapest way out and 512 MB memory is
> sufficient unless you are trying work with VERY big PDB files. If so, try
> to get your hands on a "new, see details" Quadro 4000 and a separate PNY
> 3-pin mini DIN stereo bracket (930-50764--000 C for about 20 US$) or a
> "new, see details" Quadro 5000 with build-in emitter.
>
> Good luck
>
> Jeroen.
>
>
> Am 28.11.17 um 10:50 schrieb Johannes Cramer:
>
> Hi Christine,
>
> as far as I know, it does not work at all with Geforce cards. The Nvidia
> drivers do not support windowed quad buffered GL, which you need for
> coot/pymol. It does not matter whether you use Windows or Linux.
> But this is based on my personal experience from around Oct. 2016. Maybe
> something changed quietly since then. Again, as far as I know, you need a
> Quadro card.
>
> Cheers,
> Johannes
>
> 2017-11-06 21:24 GMT+01:00 Christine Gee <chr...@gmail.com>:
>
>> Hi,
>>
>> I have looked in the archive for posts about this, but there hasn't been
>> one for about a year. Can anyone comment on whether they have managed to
>> get a linux flavor and GeForce cards to work with pymol and/or coot 3D
>> stereo? Geforce cards supposedly support openGL, but posts from October
>> last year on the BB suggests that it only works in windows unless you have
>> a monitor with a built in emitter. I would appreciate any feedback.
>>
>> Regards
>> Christine
>>
>>
>
> --
> Dr. math. et dis. nat. Jeroen R. Mesters
> Deputy, Senior Researcher & Lecturer
> Program Coordinator *Infection Biology*
> <http://www.uni-luebeck.de/studium/studiengaenge/infection-biology/introduction.html>
>
> Institute of Biochemistry, University of Lübeck
> Ratzeburger Allee 160
> <https://maps.google.com/?q=Ratzeburger+Allee+160=gmail=g>,
> 23538 Lübeck, Germany
> phone: +49-451-31013105 <+49%20451%2031013105> (secretariate -31013101)
> fax: +49-451-31013104 <+49%20451%2031013104>
>
> [image: http://jobs.zeit.de/image-upload/logo_10564.jpg]
> http://www.biochem.uni-luebeck.de 
> http://www.eine-stadt-sieht-gelb.de 
> http://www.uni-luebeck.de/studium/studiengaenge/infection-biology
> http://www.iobcr.org 
>
> Visiting Professorship in Biophysics, University of South Bohemia (CZ)
> President of the International Organization for Biological Crystallization
> (IOBCr)
> --
> If you can look into the seeds of time and tell which grain will grow and
> which will not, speak then to me who neither beg nor fear (Shakespeare's
> Macbeth, Act I, Scene 3)
> --
> "Aujourd'hui je sais qu'il n'y a pas de limites à la bêtise humaine -
> qu'elle est infinie." (Gustave Flaubert, French novelist, 1821-1880)
> --
> It is invariably the case that high resolution X-ray structures show
> significantly better agreement with solution observables such as coupling
> constants, 13C chemical shifts, and proton chemical shifts, than the
> corresponding NMR structures, including the very best ones. Hence,

Re: [ccp4bb] XDS questions

[Jim Fairman]

Wei,

The flag MAXIMUM_NUMBER_OF_PROCESSORS=
<http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#MAXIMUM_NUMBER_OF_PROCESSORS=>
in XDS.INP should allow you to choose the number of processors you wish to
use.

Cheers, Jim

------
Jim Fairman
C: 1-240-479-6575

On Thu, Nov 17, 2016 at 12:40 PM, Wei Wang <ww2...@columbia.edu> wrote:

> Hi,
>
> Is there a way to let xds_par use less than all processors/threads on the
> machine? Sometimes I would like to process something else while XDS is
> running.
>
> Another question is related to the scaling procedure. My understanding is
> that the XDS already does the scaling during correction. So if I follow the
> XDS-Aimless route, then probably I should let Aimless do "skip scaling and
> only merge"? Please elucidate me on this issue.
>
> Regards,
>
> Wei
>

Re: [ccp4bb] Generating Restraints for a Synthetic Peptide

[Jim Fairman]

Phenix should also work nicely:

phenix.elbow inputfile.smi --opt

Inputfile can be one of many different file formats (ie: smiles, sdf, pdb,
etc.)

The --opt flag runs an AM1 geometry optimization that usually produces
superior restraints as compared to running without it.

Cheers, Jim

On Tue, Jun 23, 2015, 10:27 AM Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:

 Dear Sean Fanning,

 you could try the grade server (grade.globalphasing.org). I don't know
 its size limit. It recognizes the ligand YJD from 2YJD and produces
 restraints for it.

 In your case you may need to generate the mol2 file or SMILES string. I
 think openbabel could generate the mol2 file from the PDB file, I
 haven't tried.

 Best,
 Tim

 On 06/23/2015 05:17 PM, Sean Fanning wrote:
  Dear CCP4 Users,
  I have a structure containing a synthetic alpha helical peptide (similar
 to
  the one found in PDB: 2YJD) for which I need to generate the restraints
  (.cif). I have the PDB coordinates for the peptide but need the .cif for
  refinement/fitting. Does anyone have any suggestions on how I could
  generate this file?
  Thank you very much,
  Sean Fanning
 

 --
 --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 phone: +49 (0)551 39 22149

 GPG Key ID = A46BEE1A

Re: [ccp4bb] nVidia quadro

[Jim Fairman]

Please check your part number vs. Nvidia's compatible hardware list at the
link below. Looks like it's on the list to me:

http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html

Cheers, Jim

On Mon, Mar 23, 2015 at 4:06 PM, Oganesyan, Vaheh oganesy...@medimmune.com
wrote:

   Graphics gurus,




 http://www.amazon.com/PNY-DisplayPort-Profesional-Graphics-VCQ6000-PB/dp/B0044XUD1U/ref=sr_1_8?ie=UTF8qid=1427151570sr=8-8keywords=nvidia+quadro



 Would this card work for quad buffered stereo on Linux workstation? It
 does have 3-pin mini Din.





 Regards,



 *Vaheh Oganesyan*

 *MedImmune, ADPE*

 *www.medimmune.com http://www.medimmune.com*


  To the extent this electronic communication or any of its attachments
 contain information that is not in the public domain, such information is
 considered by MedImmune to be confidential and proprietary. This
 communication is expected to be read and/or used only by the individual(s)
 for whom it is intended. If you have received this electronic communication
 in error, please reply to the sender advising of the error in transmission
 and delete the original message and any accompanying documents from your
 system immediately, without copying, reviewing or otherwise using them for
 any purpose. Thank you for your cooperation.




-- 
Jim Fairman, Ph D.
Group Leader I - Crystallography
Beryllium http://www.be4.com
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@be4.com

Re: [ccp4bb] Visualizing Stereo view

[Jim Fairman]

You can create stereo images for publications in pymol:
http://www.pymolwiki.org/index.php/Stereo_ray

Adding labels and getting them to float at the correct depth within the
image can be tricky.

As for visualizing the stereo images, you can either practice alot and get
good at cross eyed stereo viewing, or you can buy a pair of glasses to
assist you in seeing the 3d effect. If you google cross eyed stereo
glasses, you will get many options to purchase. Old chemistry texts used
to come with a pair, but I'm not sure that students actually purchase
textbooks anymore.


On Sat, Jan 17, 2015 at 23:50 PM, jeorgemarley thomas kirtswab...@gmail.com
 wrote:

Dear all,

First of all sorry to put this off topic and silly question on bb. Can
anybody suggest me, how to create a stereo image and how it is different
from the normal. How can I visualize it, if anybody has answer for this
please suggest me its significance in analysis. Thank you very much in
advance.

Thanks

Jeorge



-- 
Sent from MetroMail

Re: [ccp4bb] active 3D monitors: successor of Asus VG278HR?

[Jim Fairman]

Hi Tobias,

You most definitely do not need a built-in emitter for your system to
work.  Instead you use the little emitter temple that comes with a set of
the glasses
http://www.nvidia.com/object/product-geforce-3d-vision2-wireless-glasses-kit-us.html.
In Windows, the emitter can be driven via USB, but for Linux it will need
to be driven by the 3-pin stereo connector that plugs directly into your
Quadro-class graphics card.  You can just place the emitter anywhere that
the glasses have a clear line of sight to while you are wearing them.  I
usually pick directly underneath the screen.

The ASUS VG278HE
http://www.amazon.com/VG278HE-27-Inch-Screen-LED-lit-Monitor/dp/B00906HM6K/ref=sr_1_1?ie=UTF8qid=1420732033sr=8-1keywords=ASUS+VG278HE
 (without built in emitter) is in stock over at Amazon.

Cheers, Jim

On Thu, Jan 8, 2015 at 6:08 AM, Tobias Beck tobiasb...@gmail.com wrote:

 Dear all,

 I am looking again at 3D monitors. Last year I bought for my old lab the
 VG278HR and the PNY K600, as advised by the CCP4BB. (The 3D test images
 from Nvidia were running fine under Windows, but I did not get around to
 finish the set up with pymol and coot under linux.)

 Now at a new place, I looked at available monitors again (that have the
 built-in emitter since I want to use the K600 graphics card) and noticed
 that the VG278HR is out of stock. The VG278H, which seems to be a very
 similar model, is also out of stock.

 This page

 http://www.nvidia.com/object/3d-vision-displays.html

 also lists the Acer HN274H as a 27'' monitor with built-in emitter, but
 that seems to be out of stock as well (I would prefer not to buy a
 refurbished or used one). The monitors mentioned above are also listed
 here:

 http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo

 (The smaller BenQ XL2420TX listed there is also out of stock).

 Has anybody ordered a 3D monitor with built-in emitter recently or could
 provide me with a current list of 27'' monitors with built-in emitters? I
 checked with Nvidia via their chat support, but they did not have an
 updated list, just provided links to the manufacturers' homepages.

 If monitors with built-in emitters are not available anymore, I need to
 buy a different graphics card in order for the setup to work with linux,
 right?

 Thank you and best wishes, Tobias.

 --
 ___

 Dr. Tobias Beck
 - group leader -
 RWTH Aachen University
 Institute of Inorganic Chemistry
 Landoltweg 1, office: 304N
 52056 Aachen, Germany
 phone:  +49-241-80-90057
 fax:   +49-241-80-99003
 ___




-- 
Jim Fairman, Ph D.
Group Leader I - Crystallography
Beryllium http://www.be4.com
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

Re: [ccp4bb] Fabricating hamilton syringe coupler for LCP preparation

[Jim Fairman]

As a user of many of these coupling devices, I would highly suggest buying
your couplers pre-fabricated and avoiding many hours (and possibly days) of
headaches trying to manufacture these with your own hands.

Rigaku Reagents sells them:
https://www.rigakureagents.com/p-516-wizard-cubic-lcp-kit.aspx

Formulatrix sells them a bit cheaper:
http://formulatrix.com/store/product.php?productid=27cat=4page=1

I have used both products and they both function well even after many uses
and cleaning cycles in methanol.

Cheers, Jim



On Mon, Dec 15, 2014 at 11:09 AM, Thomas Cleveland 
thomas.clevel...@gmail.com wrote:

 Hi all,

 I'm trying to put together some homemade syringe couplers following
 the published instructions from the Caffrey group.  I'm having a bit
 of trouble with this part:

 The stainless steel ferrule of the second needle is removed and
 placed on the free end of the coupling needle such that the double
 thumb nut is held symmetrically between the two steel ferrules

 Has anyone done this, and if so, how did you remove the stainless
 steel ferrule from the second needle in order to place it over the
 first?  The stainless steel ferrule appears to be firmly attached and
 I'm having trouble removing it.

 Thanks,
 Thomas Cleveland



-- 
Jim Fairman, Ph D.
Group Leader I - Crystallography
Beryllium http://www.be4.com
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

Re: [ccp4bb] 3D monitors

[Jim Fairman]

It seems as though this topic is re-visited quite often on this discussion
board.  I would refer you to search the CCP4BB archives
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/ for an extensive
amount of discussion on this topic over the past couple of years.

A quick synopsis of an alternative to Zalman:

NVidia 3D Vision
http://www.nvidia.com/object/3d-vision-professional-users.html 'For
Professionals' (the version used for video games supports DirectX and not
OpenGL) combined with a Quadro class video card and a 120 Hz
monitor/projector that are both on NVidia's hardware compatibility list
http://www.nvidia.com/object/3d-vision-pro-requirements.html.

Cheers, Jim


On Thu, Sep 4, 2014 at 10:26 AM, Ming Luo m...@gsu.edu wrote:

 ASUS VG278HE Black 27 2ms (GTG) HDMI Widescreen LED Backlight LCD Monitor
 300 cd/m2 50,000,000:1 Built-in Speakers 3D ready, Height, Swivel adjustable

 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
 Fares Z. Najar
 Sent: Thursday, September 04, 2014 1:12 PM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] 3D monitors

 Dear all,
 I was wondering if there are 3D monitors for X-ray crystallography other
 than Zalman.

 Thanks
 Fares

 --
 Dr. Fares Z. Najar
 Research Faculty/Adjunct Professor
 Department of Chemistry and Biochemistry Stephenson Life Sciences and
 Research Center
 101 Stephenson Parkway
 Norman, OK 73019

 Email: fzna...@ou.edu




-- 
Jim Fairman, Ph D.
Group Leader I - Crystallography
Beryllium http://www.be4.com
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

Re: [ccp4bb] PyMol and Schrodinger

[Jim Fairman]

To the best of my knowledge the source code is still available on
Sourceforge:  http://sourceforge.net/projects/pymol/

You should be able to compile binaries for the OS of your choice from there.

That being said, CCP4MG has been coming along nicely in recent years - at
this point I'm 50:50 between Pymol and CCP4MG for making figures for
presentations/papers.

Cheers, Jim


On Wed, Apr 23, 2014 at 8:43 AM, Cygler, Miroslaw
miroslaw.cyg...@usask.cawrote:

  Hi,
 I have inquired at Schrodinger about the licensing for PyMol. I was
 surprised by their answer. The access to PyMol is only through a yearly
 licence. They do not offer the option of purchasing the software and using
 the obtained version without time limitation. This policy is very different
 from many other software packages, which one can use without continuing
 licensing fees and additional fees are only when an upgrade is needed. At
 least I believe that Office, EndNote, Photoshop and others are distributed
 this way.
 I also remember very vividly the Warren’s reason for developing PyMol, and
 that was the free access to the source code. He later implemented fees for
 downloading binary code specific for one’s operating system but there were
 no time restrictions on its use.
 As far as I recollect, Schrodinger took over PyMol distribution and
 development promising to continue in the same spirit.  Please correct me
 if I am wrong.
 I find the constant yearly licensing policy disturbing and will be looking
 for alternatives. I would like to hear if you have had the same experience
 and what you think about the Schrodinger policy.
 Best wishes,

 Mirek






-- 
Jim Fairman, Ph D.
Crystal Core Leader I
Emerald Bio http://www.embios.com
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

Re: [ccp4bb] off-topic: bug busting

[Jim Fairman]

I would also recommend the Emulsiflex line of cell disruptors from Avestin
- it has been my favorite and most easily used instrument of cell
destruction.


On Tue, Feb 4, 2014 at 9:17 AM, Mark J van Raaij mjvanra...@cnb.csic.eswrote:

 LOL.

 In any case, a French press is also not french, according to Wikipedia it
 was invented by Charles Stacy French of the Carnegie Institution of
 Washington (hence French press with capital F).

 In any case, I agree, Emulsiflex, Constant Systems One-shot,
 Microfluidizer etc. is the way to go if you have some money.

 Mark J van Raaij
 Lab 20B
 Dpto de Estructura de Macromoleculas
 Centro Nacional de Biotecnologia - CSIC
 c/Darwin 3
 E-28049 Madrid, Spain
 tel. (+34) 91 585 4616
 http://www.cnb.csic.es/~mjvanraaij





 On 4 Feb 2014, at 18:09, Pascal Egea wrote:

  Hi Phoebe,
 
  Another possibility is the Emulsiflex (from Avestin, in canada). Not a
 cheap piece of equipment, but very sturdy and efficient to up to 200 mL of
 extract (runs on house-air). Can deal with E coli (and even yeast if you
 have the models with internal compressor). It comes in 3 sizes I think we
 have the middle one (C-3) with a compressor. It is basically a french press
 but without the inconvenient of being french (I am french myself). It is
 quite gentle, and does not overheat samples as much as the sonicator. We
 make a lot of membrane protein purifications and I have been working with
 this since my post-doc
  Hope this helps.
 
  Best regards,
 
  Pascal Egea
 
 
  On Tue, Feb 4, 2014 at 8:49 AM, Phoebe A. Rice pr...@uchicago.edu
 wrote:
  Some time ago, there was a nice discussion of cost-effective, wimpy
 protein-friendly ways to break open E. coli.  We're thinking about
 replacing an aging sonicator.  If people have a favorite gizmo, could they
 repeat that advice?
  thank you,
Phoebe Rice
 
  ++
 
  Phoebe A. Rice
  Dept. of Biochemistry  Molecular Biology
  The University of Chicago
 
  773 834 1723; pr...@uchicago.edu
  http://bmb.bsd.uchicago.edu/Faculty_and_Research/
 
  http://www.rsc.org/shop/books/2008/9780854042722.asp
 
 
 
  --
  Pascal F. Egea, PhD
  Assistant Professor
  UCLA, David Geffen School of Medicine
  Department of Biological Chemistry
  Boyer Hall room 356
  611 Charles E Young Drive East
  Los Angeles CA 90095
  office (310)-983-3515
  lab  (310)-983-3516
  email pe...@mednet.ucla.edu




-- 
Jim Fairman, Ph D.
Crystal Core Leader I
Emerald Bio http://www.embios.com
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

Re: [ccp4bb] Off Topic: Formulatrix NT8 nanoliter-volume dispenser

[Jim Fairman]

Hi Dileep,

We have been a user of the NT8 robot going on a year now, and we're quite
happy with it.  The initial versions of the machine had a few problems, but
engineers over at Formulatrix have worked out a majority of the bugs and
the current version of the machine functions quite well.  We use it mostly
for sitting drop tray setups and for LCP crystallization - haven't
attempted any hanging drop setups, but should work fine.  My favorite
feature of this machine is the humidity controlled chamber.  You can set
the humidity level within the chamber, and sensors keep the percent
humidity within the user-specified range.  It makes evaporation problems
with LCP setups I've experienced in the past virtually non-existent.

Customer service at Formulatrix has also been very quick to reply if
anything ever does go wrong with the machine.

Hope this helps.

Cheers, Jim




On Wed, Nov 6, 2013 at 6:53 AM, Dileep V vasudevandil...@gmail.com wrote:

 Hi there:

 Has anyone got experience using the Formulatrix NT8 as a 'crystallization
 robot'? Other options being considered are Art Robbins Phoenix  TTP
 Labtech's Mosquito, both of which I have used in the past.

 Any feedback on NT8 will be highly appreciated.


 Thanks and Regards,
 Dileep







-- 
Jim Fairman, Ph D.
Crystal Core Leader I
Emerald BioStructures http://www.emeraldbiostructures.com/
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

Re: [ccp4bb] Detergent solubilization step (membrane proteins)

[Jim Fairman]

Raji,

First, I would suggest increasing the solubilization time by attempting
solubilization overnight at 4 degrees.  I would also suggest a few more
detergent choices.  In addition to DDM, my other favories are OG and
Elugent (a mixture of several detergents) for extraction from *E.
coli* membranes.
 If one of these still doesn't extract your protein of interest, you can
move onto other more exotic options.  I know it's a bit self-plugging, but
the products division of Emerald Bio sells a 96-well detergent screen you
can use to go through a wide variety of solubilization detergent options at
small scale.  We've used it in-house in our services division to get some
nice results for several of our membrane protein projects.

However, you may be fighting a losing battle as many times protein that
doesn't extract from the membranes can be misfolded or aggregated,
remaining strongly associated with the membranes.

Cheers, Jim


On Wed, Jul 10, 2013 at 2:23 PM, Raji Edayathumangalam r...@brandeis.eduwrote:

 Dear BBers,

 Sorry for the non-ccp4 post.

 I'd like to hear tips and suggestions from the membrane protein folks in
 the community.

 I am currently purifying two different membrane proteins expressed in E.
 coli. While I am able to extract practically all of my first protein from
 the cell membrane into buffer containing 1% DDM in 1hr at 4C, it doesn't
 seem as though that works very well for my second protein. I understand
 every protein is a unique beast; I am just trying to increase the yields
 for my second protein as much as possible.

 For my second protein, I have tried solubilizing for 1hr at 4C in 1% DDM
 as well as in 1-2% NM for 1hr at 4C but am only able to solubilize about
 half of total protein in the membrane. Have folks seen substantial increase
 in % solubility with longer incubations with detergent? Or should I
 consider the issue that the fraction that doesn't solubilize may be
 misfolded, just cut my losses and grow tons more bacterial cultures.

 Many thanks for sharing your successes and heartaches on this matter!
 Raji

 --
 Raji Edayathumangalam
 Instructor in Neurology, Harvard Medical School
 Research Associate, Brigham and Women's Hospital
 Visiting Research Scholar, Brandeis University




-- 
Jim Fairman, Ph D.
Crystal Core Leader I
Emerald BioStructures http://www.emeraldbiostructures.com/
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

Re: [ccp4bb] a new version of XDS

[Jim Fairman]

You can always use VMWare player to run a virtual machine of a Linux
distribution inside Windows.  It's free and it works fairly well.


On Wed, May 29, 2013 at 1:29 PM, Jacob Keller 
j-kell...@fsm.northwestern.edu wrote:

 Any thoughts of making a Windows executable? Might help a lot of users

 JPK


 On Wed, May 29, 2013 at 4:20 PM, Kay Diederichs 
 kay.diederi...@uni-konstanz.de wrote:

 ... is available for academic users at http://homes.mpimf-heidelberg.**
 mpg.de/~kabsch/xds/ http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/
 Please note that there are some incompatibilities; most notably, the new
 format of XPARM.XDS is different so that the new INTEGRATE does not work
 with an old XPARM.XDS.

 best,

 Kay




 --
 ***

 Jacob Pearson Keller, PhD

 Looger Lab/HHMI Janelia Farms Research Campus

 19700 Helix Dr, Ashburn, VA 20147

 email: kell...@janelia.hhmi.org

 ***




-- 
Jim Fairman, Ph D.
Crystal Core Leader I
Emerald BioStructures http://www.emeraldbiostructures.com/
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

Re: [ccp4bb] Membrane Protein Optimisation

[Jim Fairman]

With information you've provided I have multiple suggestions for you, some
of which you may have already tried:

1.   OMPs can be fairly particular about which detergents they will
crystallize in.  Try exchanging the protein into a different
detergent/detergent mixture and then set up new trays in your favorite
broad matrix screens.  DDM, DM, LDAO, OG, and C8E4 are a few of my
favorites for OMPs, but there are many others.  This can be done using a
size exclusion column as the final purification step for your protein where
the column is equilibrated with the appropriate detergent.  This step will
also let you know how well behaved the protein is in that detergent via the
shape/height of the peak.  This won't help you optimize your current
condition, but it may lead to different/new conditions with even better
crystals.  As Pascal suggested, try to carefully choose which MW cut-off
concentrator you end up using.  Minimizing the amount of detergent
concentration that occurs during your concentration step(s) is optimal.

2.  Attempt crystallization using DHCP/CHAPSO bicelles.  You can buy them
pre-made from MemX Biosciences or make them yourself using a published
protocol from David Bowie's lab.  These have been used to crystallize the
mitochondrial beta barrel protein VDAC and I had success crystallizing
intimin in them.  David Bowie also has a JoVE article on the bicelle
crystallization method.

3.  Attempt crystallization using Lipidic Cubic Phases.  This was the
saving grace for my post-doc project.  Neither detergent nor bicelle
crystallization produced crystals that were of sufficient quality, but the
crystals from LCP all diffracted to the 2.0 angstrom resolution range.  If
you're unfamiliar with the technique, there are several nice videos on JoVE
describing it by Vadim Cherezov and Martin Caffrey.

4.  Alter your construct.  Small changes in the construct (ie: deletion or
addition of 1-2 residues on the N- or C-terminus) often led to drastically
different crystallization behavior of several OMPs in my hands.

Cheers, Jim


On Thu, May 9, 2013 at 8:34 AM, RHYS GRINTER r.grinte...@research.gla.ac.uk
 wrote:

 Hi All,

 A quick question if you've ever worked on membrane proteins, I'm trying to
 optimize crystals for bacterial integral outer membrane protein I'm working
 on. I'm getting some fairly modest rod like crystals in a  0.1M Tris pH
 7.5, 30% PEG 600, 0.03M MgCl2 condition. However I get lots and lots of
 birefringent gel forming in the same condition, I get the feeling that this
 is Detergent/Protein complex and is robbing my crystals of material to grow
 bigger.
 These crystals diffract to 5 A so I'd quite like to make them bigger and
 better,

 Cheers,

 Rhys




-- 
Jim Fairman, Ph D.
Crystal Core Leader I
Emerald BioStructures http://www.emeraldbiostructures.com/
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

Re: [ccp4bb] lcp crystal extraction

[Jim Fairman]

Hi Konstantin,

I use #11 Classic Fine Point Blades from X-acto to cut through the
plastic Laminex film covers without much of an issue.  If you decide to use
glass covers rather than plastic, Hampton sells a nice glass-cutting tool (
http://hamptonresearch.com/product_detail.aspx?cid=18sid=203pid=626).

Cheers, Jim

On Thu, Mar 28, 2013 at 3:26 PM, Konstantin Knoblich
knobl...@wehi.edu.auwrote:

 Hi All,

 I am wondering if anyone has tried to retrieve a crystal from a Molecular
 Dimension LCP plate. What would you recommend as a method? The plastic is
 too flexible to be cut as it squashes the drop when you try it. Is there
 another way someone has successfully done this? Thanks in advance for your
 input.

 Konstantin




-- 
Jim Fairman, Ph D.
Crystal Core Leader I
Emerald BioStructures http://www.emeraldbiostructures.com/
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

Re: [ccp4bb] Please recommend linux workstation

[Jim Fairman]

I've been pretty happy with the machines from
System76https://www.system76.com/.
 They come with the most recent version of Ubuntu pre-installed.

However, as Tim says - installing Linux on any machine you can buy is a
pretty simple process now.

Cheers, Jim

On Fri, Mar 15, 2013 at 9:42 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 Dear Jie Liu,

 most Linux distributions are not too difficult to install, and with a
 decent internet connection you only need to download a few MB for a
 bootable CD for network installation - do you have a reason why you do
 not want this yourself?

 Kind regards,
 Tim

 On 03/15/2013 05:34 PM, jie liu wrote:
  Dear All
 
  I am planning to buy a linux workstation for crystallography. It
  seems that Dell does not offer workstations with linux right now.
  Any good experience to recommend?
 
  Thank you!
 
  Jie Liu
 

 - --
 - --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen

 GPG Key ID = A46BEE1A

 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.12 (GNU/Linux)
 Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

 iD8DBQFRQ09xUxlJ7aRr7hoRAvJ+AJ9OM3AiV7RixUFaNqPCMbKhkKzqlwCgomP/
 7o166epVERXwzoBe0/xp2s0=
 =SbA8
 -END PGP SIGNATURE-




-- 
Jim Fairman, Ph D.
Crystal Core Leader I
Emerald BioStructures http://www.emeraldbiostructures.com/
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

Re: [ccp4bb] the lysozyme of membrane proteins?

[Jim Fairman]

Two additional suggestions:

1. Photosynthetic Reaction Center from *R. sphaeroides* might be up your
alley.  Similar to bacteriorhodopsin, no need for a GFP tag on this one as
it's colored.  See the following publications:

Wallace et al. Monoolein Lipid phases as incorporation and inrichment
materials for membrane protein crystallization PLoS One. Aug 31 2011.
Kors et al. Effects of impurities on membrane-protein crystalllzation in
different systems Acta Cryst D Biol Crystallogr. Oct 2009. p1062-73.

2.  The beta barrel transmembrane domain of intimin would work as well.
 Expresses in standard BL21 DE3 *E. coli* cells, 3 step purification,
crystallizes readily in LCP, and is stable for months at a time at 4
degrees (not colored though):

Fairman et al. Crystal Structures of the outer membrane domain of intimin
and invasin from enterohemorrhagic *E. coli* and enteropathogenic *Y.
pseudotuberculosis*. Structure. Jul 3 2012. p 1233-43.

Cheers, Jim

On Tue, Sep 11, 2012 at 2:18 PM, Ho Leung Ng h...@hawaii.edu wrote:

 Hello,

   I am developing an undergraduate biochemistry lab class and
 would like to incorporate experiments with membrane proteins. Does
 anyone have suggestions on membrane proteins that are relatively easy
 to express, purify, and assay? Bonus points for crystallizable! At the
 moment, my leading candidate is aquaporin AqpZ from E. coli. I am
 planning to express the membrane protein as a GFP fusion so students
 can easily follow it through the course of the labs.


 Thank you,
 Ho

 Ho Leung Ng
 University of Hawaii at Manoa
 Assistant Professor, Department of Chemistry
 h...@hawaii.edu




-- 
Jim Fairman, Ph D.
Crystal Core Leader I
Emerald BioStructures http://www.emeraldbiostructures.com/
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

Re: [ccp4bb] Plastic and glass plates

[Jim Fairman]

Theresa,

The major advantage of the plastic plates is indeed ease of harvest.
 However, the plastic plates also tend to have some evaporation issues and
eventually dry out after a few months, where as the glass plates basically
last forever.  On the other hand, protein crystals in LCP tend to form in
the first several weeks after an experiment is set up so this usually isn't
a problem.  Some people prefer to set up initial screening experiments in
the glass plates and then optimize and set up farm trays using the
plastic plates where it's easier to harvest from (and cheaper).  I've also
set up everything in plastic trays from the start of a project to finish
without any problems.  If you're looking to perform LCP FRAP experiments,
glass is the best way to go.

Cheers, Jim

On Wed, Aug 29, 2012 at 12:24 PM, Theresa Hsu theresah...@live.com wrote:

 Dear all

 Is there any pros and cons of using plastic plates for LCP
 crystallization? The glass is clearer but it is very difficult to open.

 Thank you.




-- 
Jim Fairman, Ph D.
Crystal Core Leader I
Emerald BioStructures http://www.emeraldbiostructures.com/
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

Re: [ccp4bb] determination of oligomerization state of protein

[Jim Fairman]

Multi-Angle Light Scattering (MALS) coupled with an HPLC column attached to
an analytical SEC column is my standard go-to method for determining
molecular weights/oligomeric states of peaks from SEC runs.  I've only ever
used the detectors from Wyatt (
http://www.wyatt.com/solutions/hardware/hardware.html), not sure if there
are any other manufacturers in the business.

Cheers, Jim

On Mon, Aug 13, 2012 at 10:04 AM, Sangeetha Vedula
sangeetha...@gmail.comwrote:

 Hello all,

 I am working with a protein that is probably a hexamer based on homology
 with other proteins but when I ran it on an analytical size gel filtration
 column, I see multiple peaks. I would like to determine the exact
 oligomerization state of the mixture and have considered blue native gel
 electrophoresis and gradient centrifugation. The monomer is about 54 kDa.
 All of the peaks are active enzymatically. I wish I could test higher
 concentrations to see if the equilibrium will shift towards a hexamer (or
 whatever the naturally highest state is) but the protein crashes out.

 The protein was expressed in baculovirus and the multitude of states could
 be an artifact but I'd like to know what I am working with. Also, down the
 line, I'll need to pick one of the states for crystallization trials.

 Has anyone encountered this problem? How did you determine the
 oligomerization state(s)?

 I have basic biorad gel apparatus available and no gradient mixer.

 Thanks for any input.

 Best regards,

 Sangeetha.





-- 
Jim Fairman, Ph D.
Crystal Core Leader I
Emerald BioStructures http://www.emeraldbiostructures.com/
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

Re: [ccp4bb] Membrane Protein Crystallization Plates

[Jim Fairman]

Yuri,

Did you mean plates for setting up Lipidic Mesophases?  If so, here is a
listing of products I have used in the past.  I highly endorse the plates
from Molecular dimensions, particularly the plastic laminex plates
(MD11-51-100 + MD11-54).  They do have the dis-advantage of drying out
after a 2-month or so period, but they make the job of harvesting
significantly easier than dealing with the glass equivalents (so much so
that I don't ever plan on using the glass bases and covers again).

*Molecular Dimensions:*  Using the MD11-51-100 plastic bases combined with
the MD11-54 covers results in a cost of $9.20 per plate.

Laminex Plastic 100 um base (MD11-51-100) - I've used these to solve
multiple structures during my post-doc at NIH.  They're UV transparent for
doing UV microscopy and detection of your crystals.  Cost: $66 USD for a
pack of 10.

Laminex Plastic 200 um base (MD11-50) - Has a thicker 200 um layer for
inputting larger amounts of mesophase and precipitant.  Cost:  $66 USD for
a pack of 10.

Laminex Film Cover (MD11-54) - Used to cover the top of the sandwich
plate.  Also UV transparent.  Cost: $26 USD per pack of 10.

Laminex Glass 100 um base (MD11-50-100) - Glass base with 100 um spacer.
Cost:  $66 USD per pack of 10.

Laminex Glass 200 um base (MD11-50) - Glass base with 200 um spacer.  Cost:
$66 USD per pack of 10.

Glass Covers (MD11-52) - Glass for forming sandwich plates.  Cost: $40 per
pack of 10.

*Hampton Research:*

Plastic UV Transparent LCP Setup Kit (HR3-186) - Set of 20 plastic plates
in a slightly different form factor than the Mol Dim. plastic plates.
 Cost: $483 USD per pack of 20.  This is $24.15 per plate.

Glass UV Transparent LCP Setup Kit (HR3-151) - Siliconized glass bases and
glass tops.  Cost: $368 USD per pack of 20 ($18.40 per plate).



On Sat, Feb 25, 2012 at 12:35 PM, Yuri Pompeu yuri.pom...@ufl.edu wrote:

 Hello Everyone,
 I am considering the purchase of crystallization plates for membrane
 proteins.
 I would love to hear what some of the community thinks or has experienced
 with these.
 Particulalrly the monoolein and monoolein/cholesterol coated plates ( I am
 not sure I can mention the vendor here but it should not matter)
 So fire away. Is it worth it? Any succes stories? Bad experiences?
 I appreciate the input
 Best,
 Yuri




-- 
Jim Fairman, Ph D.
Crystal Core Leader I
Emerald BioStructures http://www.emeraldbiostructures.com/
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

[ccp4bb] New Faster-than-fast Fourier transform

[Jim Fairman]

New Fourier transform algorithm supposedly improves the speed of Fourier
transforms get up to a tenfold increase in speed depending upon
circumstances.  Hopefully this will get incorporated into our refinement
programs.

http://web.mit.edu/newsoffice/2012/faster-fourier-transforms-0118.html

-- 
Jim Fairman, Ph D.
Crystal Core Leader I/Project Leader I
Emerald BioStructures http://www.emeraldbiostructures.com/
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

Re: [ccp4bb] stereo

[Jim Fairman]

I run the Alienware OptX AW2310 on two of our 3D Linux workstations and it
looks spectacular. Make sure that you have a Quadro FX Nvidia video card
that is on the approved list (
http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html) with
3-pin stereo (3-pin stereo connector required for Linux, it will work
without one in Windows through USB) output and not just a normal GeForce
Nvidia card or you won't be able to run stereoscopic 3D in Linux.



One option that supports both Mac and Linux are the Zalman brand 3D
monitors.  Some people like them, some people don't.  Unless Zalman
significantly improved the technology on their monitors (ie: the right eye
can see odd numbered rows of pixels and the left eye can see even numbered
rows of pixels) you lose a significant amount of resolution from displaying
3D on these.  Due to half the pixels being drawn to each eye, the display on
the 3D Vision system using a 120 Hz monitor will look crisper and higher
quality than the equivalent Zalman monitor when displaying stereoscopic 3D.
 That being said, this solution is significantly cheaper than the Nvidia
system.



I've used and seen both and prefer the quality of the Nvidia 3D Vision, but
some people are happy with the Zalman setup.  It's really up to personal
preference as to which you will choose.

Cheers, Jim

On Wed, Sep 14, 2011 at 10:48 AM, Hena Dutta hdutt...@gmail.com wrote:

 Dear Members,

 Is any one using NVidia NVision 3D Setup with active stereo in linux
 distribution for crystallographic work? Which one would be the best choice
 to set up, an active stereo or a passive stereo for crystallographic work?
 Can anyone shade some details on this? I am planning to buy or build a new
 workstation with stereo set up. It would be great if someone can give some
 estimate on this.
 Many thanks,

 Hena




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
The Buchanan Lab http://www-mslmb.niddk.nih.gov/buchanan/index.html
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] structure based superposition

[Jim Fairman]

You can do structure based sequence alignments using STRAP. It's java based
and free.
On Aug 18, 2011 5:20 AM, Suda Ravindran biobud...@gmail.com wrote:
 Dear all,

 I would like to know the tools/servers/programs that can be used for
 structure based superposition of two or more proteins. Please help me
 out..!!

 Thanks,

 -Suda

Re: [ccp4bb] off-topic: LCD monitors

[Jim Fairman]

If you aren't aware of this, the use of 120 Hz LCDs to display stereoscopic
3D using Nvidia 3D Vision on Apple's Operating system(s) is/are not
supported: http://www.nvidia.com/object/3d-vision-pro-requirements.html

However, it will work flawlessly on Linux (or Windows if you're in the mood
for that).  I run the Alienware OptX AW2310 on two of our 3D Linux
workstations and it looks spectacular. Make sure that you have a Quadro FX
Nvidia video card with 3-pin stereo (3-pin stereo connector required for
Linux, it will work without one in Windows through USB) output and not just
a normal GeForce Nvidia card or you won't be able to run stereoscopic 3D in
Linux.

One option that supports both Mac and Linux are the Zalman brand 3D
monitors.  Some people like them, some people don't.  Unless Zalman
significantly improved the technology on their monitors (ie: the right eye
can see odd numbered rows of pixels and the left eye can see even numbered
rows of pixels) you lose a significant amount of resolution from displaying
3D on these.  Due to half the pixels being drawn to each eye, the display on
the 3D Vision system using a 120 Hz monitor will look crisper and higher
quality than the equivalent Zalman monitor when displaying stereoscopic 3D.

Cheers, Jim

On Mon, Jul 18, 2011 at 7:12 PM, Padmaja Mehta-D'souza 
padmaja-mehta-dso...@omrf.org wrote:

 Pardon the off-topic query, but I would like to get some feedback about any
 personal preference for 3D LCD monitors. I am trying to decide between the
 following 3 monitors:

 *Samsung 2233RZ* 1680 x 1050 2D and 3d Widescreen LCD Monitor

 Asus VG236H 23 2ms 1920x1080 Full HD 120Hz 3D multimedia Height  Swivel
 Adjustable WideScreen LCD

 Alienware OptX AW2310 23 3D Full HD Widescreen Monitor

 The monitor will display off of a Mac Pro Two Quad-Core Intel Xeon computer
 running both Apple and Linux OS.

 Any input will be much appreciated.

 Padmaja




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
The Buchanan Lab http://www-mslmb.niddk.nih.gov/buchanan/index.html
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] off-topic: Synchrotron look alike

[Jim Fairman]

Perhaps the shape is meant to amplify the Steve Jobs' Reality Distortion
Field?

On Thu, Jun 9, 2011 at 11:49 AM, Vellieux Frederic frederic.velli...@ibs.fr
 wrote:

 Sorry, a bit off topic. But in the news today (check google news for
 example): Steve Jobs (Apple) has revealed his plans for the new Apple
 campus (Apple headquarters) in Cupertino, California. Should look familiar
 to macromolecular crystallographers.

 Fred.




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
The Buchanan Lab http://www-mslmb.niddk.nih.gov/buchanan/index.html
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'

[Jim Fairman]

Turning off force full gpu scaling is indeed the solution to this problem
(at least it was for me).
On May 10, 2011 6:58 PM, Eric Bennett er...@pobox.com wrote:
 Nvidia lists that monitor on their list of supported hardware:
 http://www.nvidia.com/object/3d-vision-requirements.html

 They even sell some Acer monitors in their online store although they are
labeled in conflicting ways.

 I tried upgrading the driver yesterday to the 270.41.06 version but it
didn't make any difference, still only 100 Hz. Are you using Windows or
Linux? We're using the 64-bit Linux driver.

 -Eric



 On May 9, 2011, at 4:26 AM, Takaaki Fukami wrote:

 not seen a working 120 Hz stereo setup working on the Acer GD235
monitor.
 if you ask the Nvidia driver or the monitor, it reports 100 Hz instead

 This is what I encountered on Dell Alienware OptX AW2310 with Quadro
FX3800,
 which has been fixed by nVIDIA Linux driver update (in 256.44).

 I don't know if the Acer monitor is compatible or not,
 it seems better to ask NVIDIA directly. see:
 http://twitter.com/#!/NVIDIAQuadro/status/65188179753435137


 Takaaki Fukami

 -
 Discovery Platform Technology Dept. Gr.5
 Chugai Pharmaceutical Co.,Ltd.

Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'

[Jim Fairman]

1.  No you cannot use your old stereo emitter.  The 3D Vision Emitter is
required for stereo on 120 Hz LCD monitors.  You will also need new shutter
glasses from Nvidia, but these some with the emitter.  I'm not sure the
reason, but I'd guess that the older emitter can't transmit the signal at
the correct frequency to get 60 Hz to each eye.

On a side note, consider which operating system you are running on the
system to be used for stereo.  You'll need the 3-pin stereo connector if you
want to do stereo in Linux.  For Windows it isn't required.  Some computers
that Dell and other manufacturers sell with FX3800 cards don't have one
built in, and you will need to buy an adapter that hooks into the video card
to provide the port.

2.  The normal 3D Vision system uses IR signals to communicate between the
emitter and the shutter glasses.  3D Vision Pro uses RF signals for
communication between the glasses and the emitter and has a longer range and
doesn't require line-of-sight like the IR system (hence the hefty price
difference you've noticed).  I don't believe the glasses from the normal 3D
Vision kit are compatible with the 3D Vision Pro system due to the
difference in signaling systems, but I haven't tested this.  If you're going
to be sitting in front of a monitor doing modeling and don't have alot of IR
interference in the same room, the normal 3D Vision version will suffice
for your needs.  3D Vision Pro is more geared toward having large meeting
rooms and presentation halls equipped so everyone in the room can view 3D on
a large screen driven by a 120 Hz DLP projector.

3. I don't wear prescription eye glasses, but I do have long modeling
sessions without any discomfort wearing these.  They come with several
inter-changable nose-pieces so you can pick the one that fits you most
comfortably.

On Fri, May 6, 2011 at 11:27 AM, zhang yu ccp4f...@gmail.com wrote:

 Dear colleagues,

 Sorry to present the stereo issue to the board again.

 Since my old SGI CRT monitor only has 75 HZ refresh rate, the flickering in
 stereo mode bothered me a lot.  Recently, I want to update my old CRT to 120
 HZ LCD.  I have a Nvidia Quadro FX3800 in my workstation. I would like to
 make sure  some issues before I make the upgrade.

 1.  Can I apply the previous stereo emitter (Purchased from Real D, Model
 #E-2) to 120HZ LCD? Although the company told me this emitter is not
 compatible with LCD, could some one tell me why? Is it true that the Nvidia
 3D vision is the only solution for the stereo in LCD?

 2. Nvidia supply two kinds of 3D emitters. One of them is 3D vision,
 while the other one is 3D vision pro.  Which one is sufficient for
 crystallographier user? (3D vision pro is much more expensive than 3D
 vision)
 It seems that 3D vision is for home user and powered by the Nvidia
 GeForce  series graphic cards. While 3D vision pro is for professional
 user and powered by Nvidia Quardro series graphic card .

 3. It looks that the Nvidia 3D glasses are very compact. Is it comfortable
 for someone like me already with eyeglasses?


 Thanks

 Yu
 --
 Yu Zhang
 HHMI associate
 Waksman Institute, Rutgers University
 190 Frelinghuysen Rd.
 Piscataway, NJ, 08904





-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
The Buchanan Lab http://www-mslmb.niddk.nih.gov/buchanan/index.html
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

[ccp4bb] Sketcher

[Jim Fairman]

I am attempting to create a monomer with a cis-double bond using Sketcher,
but every time I tell sketcher to create the library files it makes the
double bond a trans-double bond.  Can anyone assist me with information on
how to force it to remain cis?

-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
The Buchanan Lab http://www-mslmb.niddk.nih.gov/buchanan/index.html
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Automating liquid dispensing

[Jim Fairman]

We also recently obtained a Liquidator 96 from Rainin.  Working well so far
and way below the price of any of the competitors.

On Fri, Mar 11, 2011 at 5:41 PM, Engin Özkan eoz...@stanford.edu wrote:

 Dear Stephen,

 I did start a similar thread about a year ago. If you want to see the
 posts, check this out and the responses to it:

 http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg14758.html

 In my case, the winner was the Liquidator 96 from Rainin. It has proven to
 be very useful and too popular, and now it is being utilized for everything
 under the sun.

 Best,
 Engin

 On 3/11/11 2:00 PM, Stephen McMahon wrote:

 Hi -
 We are in the market for a new liquid handling robot specifically for
 dispensing custom 96 well crystallisation screens.
 What are people using these days? Likes / dislikes?
 Many thanks,
 Stephen



 --
 Engin Özkan
 Post-doctoral Scholar
 Howard Hughes Medical Institute
 Dept of Molecular and Cellular Physiology
 279 Campus Drive, Beckman Center B173
 Stanford School of Medicine
 Stanford, CA 94305
 ph: %28650%29-498-7111(650)-498-7111




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
The Buchanan Lab http://www-mslmb.niddk.nih.gov/buchanan/index.html
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] how to install cns1.3 to mac (10.6) by fink

[Jim Fairman]

1. Go to the following URL:  http://cns-online.org/v1.3/

http://cns-online.org/v1.3/2. Click the Installation link on the
left-hand side.

3.  Follow the provided instructions for your operating system and/or shell
environment.

On Mon, Feb 7, 2011 at 6:12 PM, LISA science...@gmail.com wrote:

 Hi all,
 I installed fink 64 bit on my mac osx 10.6. I want to install cns by fink.
 I found only cns 1.3 is suitable for osx 10.6. Can someone help me to
 install this program? Thanks.
 Lisa




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
The Buchanan Lab http://www-mslmb.niddk.nih.gov/buchanan/index.html
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Full-screen stereo with Coot/PyMol/etc on 3D LCD displays?

[Jim Fairman]

Stereoscopic 3D driven by OpenGL via an Nvidia Quadro FX card is only
available on Linux and Windows.  You'll have to beg the Nvidia gods for
drivers for Mac.

On Mon, Jan 24, 2011 at 12:56 AM, Luecke, Hartmut hu...@uci.edu wrote:

 My apologies if this has been discussed before.

 Has anyone got this to work?  Preferably with a Mac?  We would love to hear
 the configuration.


 Cheers, Hudel

 Hartmut Luecke
 Director, Center for Biomembrane Systems
 Depts. of Biochemistry, Biophysics  Computer Science
 3205 McGaugh Hall
 University of California
 Irvine, CA 92697-3900
 hu...@uci.edu http://bass.bio.uci.edu/~hudel/



 This message contains confidential information and is intended only for the
 individual named. If you are not the named addressee you should not
 disseminate, distribute or copy this e-mail. Please notify the sender
 immediately by e-mail if you have received this e-mail by mistake and delete
 this e-mail from your system. E-mail transmission cannot be guaranteed to be
 secure or error-free as information could be intercepted, corrupted, lost,
 destroyed, arrive late or incomplete, or contain viruses. The sender
 therefore does not accept liability for any errors or omissions in the
 contents of this message, which arise as a result of e-mail transmission.




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
The Buchanan Lab http://www-mslmb.niddk.nih.gov/buchanan/index.html
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Full-screen stereo with Coot/PyMol/etc on 3D LCD displays?

[Jim Fairman]

Forgot to mention that this is only for the newer 120 Hz LCDs using the
Nvidia 3D Vision system.  You'll have to stick with your CRT for now or
switch to Linux/Win for the newer hardware.

On Mon, Jan 24, 2011 at 1:10 AM, Jim Fairman fairman@gmail.com wrote:

 Stereoscopic 3D driven by OpenGL via an Nvidia Quadro FX card is only
 available on Linux and Windows.  You'll have to beg the Nvidia gods for
 drivers for Mac.


 On Mon, Jan 24, 2011 at 12:56 AM, Luecke, Hartmut hu...@uci.edu wrote:

 My apologies if this has been discussed before.

 Has anyone got this to work?  Preferably with a Mac?  We would love to
 hear
 the configuration.


 Cheers, Hudel

 Hartmut Luecke
 Director, Center for Biomembrane Systems
 Depts. of Biochemistry, Biophysics  Computer Science
 3205 McGaugh Hall
 University of California
 Irvine, CA 92697-3900
 hu...@uci.edu http://bass.bio.uci.edu/~hudel/



 This message contains confidential information and is intended only for
 the individual named. If you are not the named addressee you should not
 disseminate, distribute or copy this e-mail. Please notify the sender
 immediately by e-mail if you have received this e-mail by mistake and delete
 this e-mail from your system. E-mail transmission cannot be guaranteed to be
 secure or error-free as information could be intercepted, corrupted, lost,
 destroyed, arrive late or incomplete, or contain viruses. The sender
 therefore does not accept liability for any errors or omissions in the
 contents of this message, which arise as a result of e-mail transmission.




 --
 Jim Fairman, Ph D.
 Post-Doctoral Fellow
 National Institutes of Health - NIDDK
 The Buchanan Lab http://www-mslmb.niddk.nih.gov/buchanan/index.html
 Lab: 1-301-594-9229
 E-mail: fairman@gmail.com james.fair...@nih.gov




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
The Buchanan Lab http://www-mslmb.niddk.nih.gov/buchanan/index.html
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Question on calculation of RMSD

[Jim Fairman]

Raj,

There are many programs that will give you an RMSD per residue difference
between your bound and un-bound protein.  Some will even write the RMSDs to
the B-factor column of your PDB.  You can then visualize regions in your
protein that have structural changes/movement in the bound vs. unbound by
using B-factor putty in Pymol or coloring by B-factor.

I refer you to a previous post on the subject in the CCP4BB archives:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg14496.html

On Mon, Nov 15, 2010 at 1:07 PM, Goragot Wisedchaisri 
gora...@u.washington.edu wrote:

 I would first calculate least square superposition of the first monomer
 between 2 structures (one to be fixed and one to be moved) using a program
 such as lsqkap or any other programs suggested by others. You may need to
 define a relevant region for the superimposition.

 Then take the output of the moved structure and calculate another least
 square superposition of the second monomer in the dimer to the second
 monemer of the fixed structure. Look at the rotation and translation matrix
 from the output (or log file). That will give you information of how the
 second monomer is different in the 2 structures. You can calculate the
 orientation difference (in degrees) from trace of the rotation matrix.

 Alternatively, after the first monomers are superimposed, you can use
 program lsqman (or other programs that calculate rmsd of the second monomers
 without doing least square superposition) if you prefer an rmsd value
 instead of a rotational angle.

 George Wisedchasri

 On Sun, 14 Nov 2010, E rajakumar wrote:

  Dear All
 I have two structures of homo-dimeric protein complex with different DNA.
 I want to calculate RMS deviation between second monomer from these two
 complexes by fixing superposed first monomer.

 This I require to know what is the effect of DNA on relative orientation
 of two monomers in the dimer.

 Previously I was using MOLEMAN2 to do this calculation.

 Please can you suggest me any other program to do this calculation.

 Thanking you
 Raj


 E. Rajakumara
 Postdoctoral Fellow  Strcutural Biology Program  Memorial Sloan-Kettering
 Cancer Center  New York-10021  NY  001 212 639 7986 (Lab)  001 917 674 6266
 (Mobile)




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Hardware question

[Jim Fairman]

Don't get ripped off by Dell!  Their drives aren't any faster or better
quality than the competition (IMHO they're probably slower and/or lower
quality).  If you're looking for a 2 terabyte drive, I have seven Hitachi
7K2000 2 TB (http://www.newegg.com/Product/Product.aspx?Item=N82E16822145298)
drives
in a RAID6 array inside a Thecus 7700 NAS (
http://www.thecus.com/products_over.php?cid=11pid=82set_language=english)
for 10 terabytes of storage where 2 of the drives can simultaneously fail
and still retain all the data.I have had the drives installed for over a
year now and not a single problem.

On Tue, Oct 26, 2010 at 9:52 PM, Edward A. Berry ber...@upstate.edu wrote:

 Another question about computer hardware- If I configure a computer at the
 Dell site, it costs about $700 to add a 2TB SATA drive.
 On amazon.com or Staples or such, a 2TB drive costs ~$110. to $200
 depending on brand.

 Are the Dell-installed drives much faster, or more reliable, or have
 a better warranty?  After all, RAID is supposed to stand for redundant
 array of inexpensive disks, and we could afford a lot more redundancy
 at the Amazon.com price.

 And, are there any brands or models that should be avoided due to known
 reliability issues?

 Thanks,
 eab




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Refinement

[Jim Fairman]

Did you check your data for twinning and/or pseudo symmetry using
phenix.xtriage or Pointless?  If the space group is incorrect, these
programs will also assist you in selecting the correct one.  What were the
Z-scores for the rotation and translation functions?

On Mon, Oct 18, 2010 at 7:39 PM, Jyotica Batra batra.jyot...@mayo.eduwrote:

 Hi All

 I have a dataset at 1.9A, spacegroup-P212121 (unit cell: 37.7, 39.52,
 231.72, 90, 90, 90),
 I used MR phaser and got a structure solution with LLG= 320 (1copy/a.u) .
  During refinement, the R-free (50%) and R-factors (42%) never go down.
 I have tried refining in phenix and refmac both, but still the high R-free
 problem persists.  At this point I'm seeking help to know the possible
 reasons for this high R-free.

 Thanks in advance!

 Jyotica





-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Graphics for notebook

[Jim Fairman]

The Quadro FX 3700M in my Dell Precision 6400M notebook works great with
stereo in Windows, no support for Linux yet though.

On Mon, Sep 20, 2010 at 8:57 AM, Schubert, Carsten [PRDUS] 
cschu...@its.jnj.com wrote:

 Eric,

 if you want to use stereo on a notebook you have very limited options. I
 have stereo running using a Lenovo T61p with a Nvidia Quadro FX570M under
 XP, not tried Linux yet. Officially this card is not even supported by
 Nvidia for 3D application, but works anyway in conjunction with a docking
 station, which has a DVI adaptor. Don't go with a Quadro NV series, they did
 not work in our hands.

 HTH

Carsten



  -Original Message-
  From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
  Eric Karg
  Sent: Sunday, September 19, 2010 11:46 AM
  To: CCP4BB@JISCMAIL.AC.UK
  Subject: [ccp4bb] Graphics for notebook
 
  Dear all,
 
  I wanted to know which type of graphics card is more suitable for a
  notebook which is going to be used for structural biology. Integrated
  or dedicated? ATI or NVIDIA? At the moment I have to choose between an
  integrated Intel HD Graphics or a dedicated NVIDIA NVS 3100M Graphics.
  Any suggestions are highly appreciated.
 
  Thanks!
 
  Eric




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Crystal growth time lapse movies.

[Jim Fairman]

There is a good one of lysozyme crystal growth on Bernhard Rupp's website:
http://www.ruppweb.org/level1/movies_list.htm

http://www.ruppweb.org/level1/movies_list.htmThe Microcrystallization
movie taken with the Cryscam is the one I speak of.

On Wed, Jul 21, 2010 at 11:40 AM, David Briggs drdavidcbri...@gmail.comwrote:

 Hi all

 I'm doing a quick talk on crystals/crystallography for a lay
 audience in a couple of weeks time, and I'm looking for some time
 lapse movies / animated gifs of crystal growth.

 The one I was thinking of using was here:
 http://microgravity.msfc.nasa.gov/snell/vibration.html

 But that link is broken, and I can't find it via googling.

 Does anybody know of any / have any good ones that I can beg/steal/borrow?

 Cheers in advance,

 Dave


 
 David C. Briggs PhD
 Father, Structural Biologist and Sceptic
 
 University of Manchester E-mail:
 david.c.bri...@manchester.ac.uk
 
 http://manchester.academia.edu/DavidBriggs (v.sensible)
 http://xtaldave.wordpress.com/ (sensible)
 http://xtaldave.posterous.com/ (less sensible)
 Twitter: @xtaldave
 Skype: DocDCB
 




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Cell: 1-865-748-8672
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] CCP4

[Jim Fairman]

I suggest using the PRODRG Server: http://davapc1.bioch.dundee.ac.uk/prodrg/

On Wed, Jun 9, 2010 at 7:22 AM, Matthias Zebisch 
matthias.zebi...@bbz.uni-leipzig.de wrote:

 Hi Yahui!

 I am having this problem as well again and agin. Most problematic is it, if
 you have non-standard atoms in your compound.
 I don't really know whrere the problem lies, but here is what I do:
 Do not use sketcher!
 Simply generate your ligand using coot by placing atoms into the density
 (you may start from standard compounds if available).
 Save your ligand in a pdb file and make sure (text editor), that all atoms
 belong to the same compound indicated by the same 3 letter identfier (e.g.
 LIG).
 Merge this PDB file with your protein in Coot and save.
 Run Refmac.
 Refmac will abort but before stopping it will put out a library file with
 recommended bonds and angles and so on.
 This file you should manually edit putting in your chemical knowlege of the
 ligand.

 Use this cif file in a second run for refmac and for all coot real space
 refinements.

 Have fun,

 Matthias

 PS: sometimes (no non-standard atoms) a simpler way is to leave the field
 Regularize with Refmac unchecked, when you create your final library file.


 Am 6/9/2010 12:23 PM, schrieb Yahui Yan:


 Hello,

 Could you please help me with the sketcher?

 I'm trying to use ccp4 sketcher to generate a new ligand and then complex
 it with a protein in coot.  I've drawn the ligand, numbered each atom and
 defined each bond type. Then I ran save file, create library description.
 The pdb file was loaded to coot and worked fine. Then I imported cif file.
 However, when I tried to refine the ligand, a message popped out, saying 'No
 restrains'.  I double checked the numbering, I think it's Ok. Did I do
 anything wrong? I'm really struggling on this. If you need more information,
 please let me know. Thanks very much.

 Best regards,
 Yahui



 --
 
 Dr. Matthias Zebisch
 Universität Leipzig
 Biotechnologisch-Biomedizinisches Zentrum
 Strukturanalytik von Biopolymeren
 Deutscher Platz 5
 04103 Leipzig
 Germany
 Phone: 0049-341-97-31323 (lab) -31312 (office)
 Fax  : 0049-341-97-31319
 email: matthias.zebi...@bbz.uni-leipzig.de
 




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Cell: 1-865-748-8672
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Structure Based Sequence Alignment

[Jim Fairman]

I would also recommend STRAP if you haven't tried it (
http://www.bioinformatics.org/strap/)

On Tue, May 25, 2010 at 2:53 PM, Jürgen Bosch jubo...@jhsph.edu wrote:

 http://ww2.cs.mu.oz.au/~arun/Site/mustang.html


 http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi?stage1=1daction=EXPRESSO(3DCoffee)::Regular

 or maybe what you are searching for is Consurf ?
 http://consurf.tau.ac.il/

 Jürgen

 On May 25, 2010, at 2:39 PM, Muhammed bashir Khan wrote:

 Dear All;

 Can some body tell me a website for structure based sequence alignment,
 which can also pin point the similar and identical residues in different
 colors.

 regards

 Bashir




 --
 Muhammad Bashir Khan
 Department for Biomolecular Structural Chemistry
 Max F. Perutz Laboratories
 University of Vienna
 Campus Vienna Biocenter 5
 A-1030 Vienna
 Austria

 Phone: +43(1)427752224
 Fax: +43(1)42779522


 -
 Jürgen Bosch
 Johns Hopkins Bloomberg School of Public Health
 Department of Biochemistry  Molecular Biology
 Johns Hopkins Malaria Research Institute
 615 North Wolfe Street, W8708
 Baltimore, MD 21205
 Phone: +1-410-614-4742
 Lab:  +1-410-614-4894
 Fax:  +1-410-955-3655
 http://web.mac.com/bosch_lab/ http://web.me.com/bosch_lab/




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Cell: 1-865-748-8672
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Multiple conformations of disulfide-linked cysteines

[Jim Fairman]

I have a similar situation so I am also curious for the answer.  Refmac will
always try to form a disulfide bond with both conformers for me as well.

On Mon, Mar 8, 2010 at 4:55 PM, Critton, David david_crit...@brown.eduwrote:

 Dear CCP4BB,

 I am building a protein structure containing a pair of cysteines linked via
 disulfide bond. This disulfide bond (i.e. the cysteine S-gamma atoms)
 refines well at 2/3 occupancy, however the electron density suggests that
 these cysteines each adopt a second, unlinked conformation (presumably at
 1/3 occupancy). I have no trouble building the alternate conformers;
 however, refinement causes both conformers to disulfide-bond.

 I would like to know if there is a way (and how) to specify individual
 conformers (or individual atoms) in the SSBOND record of a PDB.

 Thank you in advance,
 David A. Critton
 Graduate Student, Page Laboratory
 Department of Molecular Biology, Cell Biology  Biochemistry
 Brown University
 Providence, RI




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Cell: 1-865-748-8672
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] linux question

[Jim Fairman]

I think a good option would be to use VMWare Player to run a flavor of Linux
within Windows (http://www.vmware.com/products/player/).  Using VMware
player, you can run any flavor of linux or windows within a window in your
native OS (be it windows, mac, or any flavor of linux).  I use it to run
Ubuntu in a window inside of Windows 7 for CCP4, phenix, etc and it works
pretty flawless so far.  You can also run as many different linuxes as you
want within your native OS (ie: If you want to try out Suse, Ubuntu, Red Hat
and CentOS you can install all 4 of them on your system using VMWare within
your native OS).

On Sat, Feb 27, 2010 at 10:10 PM, David Roberts drobe...@depauw.edu wrote:

 I have a quick question about linux for all.  Is there anybody running a
 windows pc with linux on a bootable cd or bootable drive/flash drive/???
 that works for crystallography apps?  I have a colleague who does molecular
 dynamics calculations and he needs some conversion programs that are unix
 based (not pc based - they just haven't been ported and that's not my area).
  We have linux computers that he can use, but I thought in the end it might
 be easiest if he could just boot up a linux flash drive to run his
 conversion, then go back to his pc and windows.  Something like damn small
 linux or ??

 Any thoughts on this?  Thanks

 Dave




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Cell: 1-865-748-8672
Lab: 1-301-594-9229
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Electron density improvement with resolution graphic

[Jim Fairman]

You can find one here on the Cambridge X-ray crystallography course website:
 http://www-structmed.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html

On Fri, Dec 4, 2009 at 8:25 PM, Brad Bennett bradbennet...@gmail.comwrote:

 Hi all-
 I recall seeing a long time ago a figure which showed the progressive
 improvement of electron density as one increases resolution, say from 6 to
 3.5 to 2A. I believe I've seen two versions- one a larger scale pic showing
 the ability to model side chains of alpha helices at higher resolutions and
 the other a simpler graphic of a tyrosine aromatic ring showing the electron
 density hole in the middle of the ring once near atomic resolution maps are
 obtained. Does anyone have, in their teaching notes or a textbook or
 presentation, a graphic which displays this? I need it for a talk this
 weekend and Google searches have come up blank. If all else fails, I can
 generate it myself...(lazy sigh)

 Thanks in advance-
 Brad




-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Cell: 1-865-748-8672
Lab: 1-301-594-9230
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Zalman monitor on Linux and Coot

[Jim Fairman]

I can personally verify that the new Nvidia 3D Vision system on 120 Hz LCD
monitors and a Nvidia Quadro FX Video Card display stereo flawlessly in
Pymol, Wincoot,  UCSD Chimerica, and any other application that uses OpenGL
or Direct3D as its display media within both Windows Vista and Windows 7
(Nvidia documentation says it will also work in Windows XP, but I have not
tested this).  This will not work in any Linux distributions yet (as far as
I am aware), but here's to hoping they develop the drivers soon.

Here are a few links:

1.  Nvidia 3D Vision Webpage:
http://www.nvidia.com/object/3D_Vision_Overview.html
2.  Nvidia 3D Vision and QuadroFX Video Cards:
http://www.nvidia.com/object/quadro_pro_graphics_boards.html

Cheers, Jim

On Wed, Nov 4, 2009 at 10:26 AM, Justin Hall hallj...@onid.orst.edu wrote:

 Hi Ajit;

 One of our CRT monitors broke recently, and in the context of bemoaning the
 loss to a friend I was told that LCD monitors will not work for stereo
 viewing. I understood the reason to be related to the difference in refresh
 rates (?), with LCD's not being fast enough so that the viewer is left
 seeing ghosts. The effect, which I have not seen first hand, was described
 to me as capable of making most hapless stereo viewers very ill, very fast.
 I would encourage you to plumb the depths of knowledge on this subject
 further, but that is my simple understanding.

 Best wishes~

 ~Justin


 Quoting Ajit Datta adat...@jhmi.edu:

  Hello everyone,
Sorry for a non-CCP4 related question again. Can anyone let me know how
 to make stereo work on linux with Zalman monitor with Coot? Is it as simple
 as what we do with CRT monitors? Or do we need something else? We presently
 use CRT monitors on a Quadro FX 4600 graphics card. I would like to move to
 LCDs.

 Thanks for all inputs

 Ajit B.





-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Cell: 1-866-748-8672
Lab: 1-301-594-9230
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Help with improving these crystals

[Jim Fairman]

Have you tried microseeding or macroseeding?  The original crystals
for my Ph D project only diffracted to ~8 angstroms.  Microseeding
gave crystals that eventually diffracted to ~2.0.

Here are two refs that might be useful:

Bergfors, T. (2003). Seeds to crystals. J Struct Biol 142(1): 66-76.

Luft, J. R. and G. T. DeTitta (1999). A method to produce microseed
stock for use in the
crystallization of biological macromolecules. Acta Crystallogr D Biol
Crystallogr 55(Pt 5): 988-93.


On Wed, Sep 9, 2009 at 11:36 AM, Narayanan Ramasubburamas...@umdnj.edu wrote:
 Dear All:
 We have been struggling to improve the crystals shown in the attachment.
 These crystals form from a protein solution 8 mg/mL (before drop), drop
 sizes are 2 microL of protein + 2 microL of well solution (0.1 MES buffer,
 pH 6.5, 1.8 M Ammonium sulfate with 12 mM CoCl2).

 The protein was dissolved initially in 20 mM Tris.HCl, pH 8.0 containing 1
 mM EDTA.

 Low cobalt also gives smaller crystals. These diffract up to 8 A.

 Any suggestions to improve these crystals would be most welcome.

 Subbu

 PS: We have used many additives (Hampton Research - including detergent
 additives) to alter the morphology but with little success.




-- 
Jim Fairman
Postdoctoral Research Assistant
Case Western Reserve University
216-368-3337 jxf...@case.edu

Re: [ccp4bb] OpenGL Stereo 3D on 120 Hz LCDs, at last!

[Jim Fairman]

Just got this working on a machine with a Quadro FX 3800.  Stereo looks
great on both Pymol (v1.1) and the latest build of WinCoot (v0.6 build
2172).

On Fri, Jul 17, 2009 at 1:20 AM, Warren DeLano war...@delsci.com wrote:

  FYI, for folks not subscribed to pymol-users:



 nVidia today released beta drivers which at last enable OpenGL-based stereo
 3D visualization on 120 Hz LCDs using Quadro graphics cards.  So long as you
 are willing to put up with Windows, you can finally abandon those old CRTs
 without spending a fortune and without sacrificing quality of the stereo 3D
 effect.



 Details posted at http://www.pymol.org



 Cheers,

 Warren






-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 jfair...@utk.edu james.fair...@case.edu

Re: [ccp4bb] OpenGL Stereo 3D on 120 Hz LCDs, at last!

[Jim Fairman]

Warren,
Do you have a link to the beta drivers?


On Fri, Jul 17, 2009 at 1:20 AM, Warren DeLano war...@delsci.com wrote:

  FYI, for folks not subscribed to pymol-users:



 nVidia today released beta drivers which at last enable OpenGL-based stereo
 3D visualization on 120 Hz LCDs using Quadro graphics cards.  So long as you
 are willing to put up with Windows, you can finally abandon those old CRTs
 without spending a fortune and without sacrificing quality of the stereo 3D
 effect.



 Details posted at http://www.pymol.org



 Cheers,

 Warren






-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 jfair...@utk.edu james.fair...@case.edu

Re: [ccp4bb] Coot question

[Jim Fairman]

You can change the color of any map or molecule to any color you wish by
using the Map Colour and Bond Colour menus.  After you have opened a map or
molecular model simply go to the Edit menu at the top of the window;  Map
Colour will be the top option and Bond Colour will be the third from the
top.
Cheers, Jim

On Tue, Jul 14, 2009 at 12:50 PM, James Tucker Swindell II 
jtswi...@secsg.uga.edu wrote:

  Greetings all

 I am trying to change the color scheme Coot uses when opening PDB files.
 When I open two seperate PDB files in the same session I would like to
 change the colors such that there is a clear and distinct difference between
 the two chains (coot does not always do this), ie red and green instead of
 Coot offering me green and light green.

 I am comparing two different maps which are quite similar so the
 distinction is needed.

 Any ideas?

 James




-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 jfair...@utk.edu james.fair...@case.edu

Re: [ccp4bb] two identical proteins in one asymmetric unit

[Jim Fairman]

Sang Hoon,

Each molecule in the asymmetric unit is most likely different.  I work on a
protein that crystallizes as a homodimer with 2 molecules per asymmetric
unit and there are some differences between the two (eg: electron density
visible for the 14 N-terminal residues in one molecule, but not the other).

Cheers, Jim

On Tue, Mar 24, 2009 at 11:03 AM, Folmer Fredslund folm...@gmail.comwrote:

 Dear Sang

 They are really different!

 And I guess you would probably want to use NCS restraints depending on
 your resolution.

 Regards,
 Folmer

 2009/3/24 Sang Hoon Joo s...@duke.edu:
  I am refining my crystal structure in which I have two identical
  chains in one asymmetric unit.
  Space group is H32 and each chain yields me a biological trimer as
 expected.
  The problem is, do I have to assume they are identical, or they are
  really different.
  After each cycle of refinement, if I try to align two molecules I get
  ~ 0.17 RMSD.
  --
  Sang Hoon Joo, PhD
  Postdoctoral Associate
  Duke University
  239 Nanaline H. Duke
  Box 3711, DUMC
  Durham, NC 27710
 




-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 jfair...@utk.edu james.fair...@case.edu

Re: [ccp4bb] surface area calcualtion

[Jim Fairman]

Thomas,

The Areaimol program within the CCP4 suite should do what you're looking
for: http://www.ccp4.ac.uk/html/areaimol.html  Although its a calculation of
surface accessability, you can delete sections of your protein to get at the
buried area between two sections of your protein.

Cheers, Jim

On Fri, Mar 20, 2009 at 2:48 PM, Jhon Thomas jhon1.tho...@gmail.com wrote:

 Hello all

 can any one suggest any server or tool which can calculate the burried
 surface area between the domains of the same monomer? PISA calculates the
 interfacial surace area between the monomer or oligomer. Can areamol
 calculate it?

 Thanks in advance

 Thomas




-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 jfair...@utk.edu james.fair...@case.edu

[ccp4bb] Van der Waals Interaction Distances

[Jim Fairman]

Fellow CCP4 Board Members,

What is the general consensus of the structural biology community for a
range of distances that would be considered a Van der Waals
contact/interaction (eg: hydrogen bonds are usually considered to be 2.5-3.5
angstroms not including the hydrogen atoms)?

Cheers, Jim

-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 jfair...@utk.edu james.fair...@case.edu

Re: [ccp4bb] [OFF TOPIC] his-tag doesn't bind

[Jim Fairman]

You can also try TALON cobalt affinity resin from Clontech (
http://www.clontech.com/products/detail.asp?product_id=10588tabno=2) or the
high yield PrepEase resin from USB (
http://www.usbweb.com/category.asp?special=cat=234id=78806).

On Tue, Jan 27, 2009 at 4:34 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:

 Hi Fred,

 I used to worked with a protein which would not bind to the Qiagen
 NiNTA (really *NOT*) but beautifully to IDA resin (e.g. Amersham
 Pharmacia).

 This was under non-denaturing conditions, though, and I don't know whether
 this applies to the denatured state. It may be worth a try.

 Tim

 --
 Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen

 GPG Key ID = A46BEE1A


 On Tue, 27 Jan 2009, Fred wrote:

  Hi ccp4 list,
 I am trying to purify a his-tag protein by metal affinity chromatography.
 The protein was expressed in inclusion bodies and its his-tag doesn't bind
 the Qiagen Ni resin in denatured conditions (urea 8M or GndHCl 6M). Playing
 with NaCl and detergents didn't help much.
 Any help is appreciated.
 Fred




-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 jfair...@utk.edu james.fair...@case.edu

Re: [ccp4bb] [OFF TOPIC] his-tag doesn't bind

[Jim Fairman]

To go along with the EDTA comment, did you check the pH of your binding
solution?  Sometimes lysing E. coli causes the pH to drop below the pKa of
the histidines.

On Tue, Jan 27, 2009 at 8:10 PM, James Stroud xtald...@gmail.com wrote:

 You don't have EDTA left over from your protease inhibitor, do you? Some
 commercial cocktails include it. You may have to read the fine print.

 James


 On Jan 27, 2009, at 1:00 PM, Fred wrote:

  Hi ccp4 list,
 I am trying to purify a his-tag protein by metal affinity chromatography.
 The protein was expressed in inclusion bodies and its his-tag doesn't bind
 the Qiagen Ni resin in denatured conditions (urea 8M or GndHCl 6M). Playing
 with NaCl and detergents didn't help much.
 Any help is appreciated.
 Fred




-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 jfair...@utk.edu james.fair...@case.edu

Re: [ccp4bb] Affordable 3D LCD Arriving Soon

[Jim Fairman]

The problem with the iZ3D monitor is its requirement for Windows and its
related API DirectX.  This rules out alot of the crystallography community
becuase of their affinity for Linux and Mac.

On Thu, Jan 8, 2009 at 11:38 AM, Christopher Bahl ccp4.b...@gmail.comwrote:

 The 3D LCDs have been out for about a year now.  They started at around
 $700, but you can find them for about $350 now.
 http://computershopper.com/lcd-monitors/reviews/iz3d-lcd-monitor

 It's a different technology than the shutter glasses- If I understand it
 correctly, it basically uses the same principle as a 3D movie...
 http://iz3d.com/t-3dproductex.aspx

 Does anyone have an idea as to how long it will be until this is supported
 by coot/chimera/ccp4mg/VMD, etc.?

 -Chris




 James M. Vergis wrote:

 I came across an article about Samsung's  $400 3D LCD monitor coming out
 in April so I thought I'd pass it on for those who may be interested.
 http://www.engadget.com/2009/01/07/samsung-officially-introduces-2233rz-the-22-inch-3d-panel-for-g/

 I'm pretty sure their 3D implementation is different than the current
 shutter-glasses active 3D.  Hopefully it will be supported by coot and other
 3D programs.




-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 jfair...@utk.edu james.fair...@case.edu

Re: [ccp4bb] O/T: microscopes

[Jim Fairman]

Clint,

We have a Leica MZ125 scope with a Leica KL1500 LCD lightsource.  It has
adjustable zoom from 8x to 160x with the 16x occular lenses but can do up to
640x with a different occular.  We also opted for the optional optical
micrometer and polarizing lenses for looking at birefringence.
Additionally, they sell an attachment for hooking up a digital camera to
take pictures of your crystals.

This scope went for about 8k or so a year ago which is a little more than
you're looking to spend but the optics are great and it beats out any scope
I've used thus far even though I've only been doing crystallography for 4
years.

Cheers, Jim

On Tue, Dec 16, 2008 at 2:00 PM, Clint Spiegel spie...@biology.ucsc.eduwrote:

 Hi,

 I am looking to buy a modestly-priced zoom scope for x-ray
 crystallographic purposes ($2-3000).  Does anyone have suggestions about
 what/where to possibly find this?  I currently have a cheap one that goes
 from 7.5-50X, but I'd like something with a little more magnification, a
 better light source and better optics.

 Thanks,
 Clint


 Clint Spiegel
 Assistant Professor, Chemistry
 Western Washington University
 516 High Street
 Bellingham, WA 98225-9150.




-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 jfair...@utk.edu james.fair...@case.edu

Re: [ccp4bb] suggestions for UV spectrometer

[Jim Fairman]

We use a Beckman Coulter DU730.  It has a small footprint if lab space is an
issue.  It will do single-wavelength, multi-wavelength, or take an entire
spectrum in 0.5 nm steps if you desire.  It comes with the standard 1 ml
cuvette holder, but we also purchased the microcuvette accessory for volumes
in the 100 uL range.  We've been using the instrument for over a year now
with no problems.  Results for determining protein concentrations using the
method of Pace et al * *Protein
Sci.javascript:AL_get(this,%20'jour',%20'Protein%20Sci.');1995
Nov;4(11):2411-23 are very reproducible using this spec.

On Thu, Dec 4, 2008 at 10:37 AM, James M. Vergis [EMAIL PROTECTED]wrote:

 I would also recommend the nanodrop.  It takes a whole spectra every
 measurement and there is no need to dilute your sample.  You can demo it
 for
 a week and try it out.


 
 James M. Vergis, Ph.D.
 University of Virginia Molecular Physiology and Biological Physics
 MKWEINR 360A Snyder Building
 480 Ray C. Hunt Drive
 PO Box  800886
 Charlottesville, VA 22908-0886
 phone: 434-243-2730   FAX: 434-243-8271
 [EMAIL PROTECTED]
 


 -Original Message-
 From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Tim
 Gruene
 Sent: Thursday, December 04, 2008 10:16 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] suggestions for UV spectrometer

 Dear all,

 we would like to purchase a UV spectrometer for measuring protein
 concentrations (280nm), and I would like to here your comments and
 especially recommendations.

 We don't need anything fancy, a small, fast device would be sufficient.

 Tim


 --
 Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen

 GPG Key ID = A46BEE1A




-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 [EMAIL PROTECTED] [EMAIL PROTECTED]

Re: [ccp4bb] Channel inside a protein

[Jim Fairman]

Priya,

We have used a program called CAVER to find channels and cavities in our
protein.  You can download it and get instructions on its use at
http://loschmidt.chemi.muni.cz/caver/

On Mon, Nov 10, 2008 at 10:21 AM, hari jayaram [EMAIL PROTECTED] wrote:

 Hi Priya ,

 I would recommend MOLE from the list kindly compiled by Jiamudu on the
 CCP4 wikiThe list is available at the link 
 belowhttp://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Programs_for_representing_the_surface_of_a_channel_inside_protein


 http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Programs_for_representing_the_surface_of_a_channel_inside_protein


 Hari


 On Mon, Nov 10, 2008 at 9:16 AM, Priya Mudgal [EMAIL PROTECTED]wrote:

 Hello All,

 Is there any program that can find if there is a channel inside a protein?
 I also would like to know what are the alternative ways to find out a
 channel inside a protein.

 Thanks a lot.

 Priya





-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 [EMAIL PROTECTED] [EMAIL PROTECTED]

[ccp4bb] TLS Refinement on ~3 angstrom resolution structures

[Jim Fairman]

Hello everyone,

I have two structures of a protein bound to two different small molecules I
am trying to refine with REFMAC5 from CCP4 v6.0.0.  One has a resolution of
3.2 and the other has a resolution of 2.9.  If I use TLS refinement
parameters on these structures I can get the Rwork/Rfree down to 19.5/26.4
(3.2 angstrom) and 20.7/27.5 (2.9 angstrom).  Without TLS refinement the
Rwork/Rfree are 21.2/29.1 (3.2 angstrom) 22.2/27.5 (2.9 angstrom).  The
question I have is in regards to the Bfactors for these refinements.  The
average Bfactors are approximately 100 for the 3.2 angstrom structure and 70
for the 2.9 angstrom structure (These are the residual Bfactors before using
TLSANL to calculate the full Bfactor with the addition of the TLS
contribution) according to Baverage from CCP4.  These Bfactors seem very
high to me, are they acceptable for publication?  Is TLS refinement
appropriate in my case with my resolution (I read a paper from Sandalova et
al. 2001 PNAS p 9533-8 where they performed TLS refinement at 3.0 angstrom
resolution)?  Any suggestions are welcome!

Cheers, Jim

-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 [EMAIL PROTECTED] [EMAIL PROTECTED]

Re: [ccp4bb] Protein concentration

[Jim Fairman]

Mark,

There are two very easy alternatives.  First is the Bradford Coomassie Dye
binding assay.  You can buy a kit from Biorad at the following link:
http://www.bio-rad.com/B2B/BioRad/product/br_category.jsp?BV_SessionID=0349900713.1219329576BV_EngineID=ccchadeemgdfflfcfngcfkmdhkkdfll.0categoryPath=%2fCatalogs%2fLife+Science+Research%2fSample+Quantitation%2fProtein+Assay+Kits+and+Cuvettes%2fBio-Rad+Protein+AssaydivName=CorporateloggedIn=falselang=Englishcountry=HQcatLevel=5catOID=-12777isPA=falseserviceLevel=Lit+RequestsearchStr=coomassiecateName=Ordering+Information

Second is the BCA assay which can be purchased from Pierce (now bought out
by Thermo/Fisher):
http://www.piercenet.com/Products/Browse.cfm?fldID=02020101

Cheers, Jim

On Thu, Aug 21, 2008 at 6:54 AM, Mark Hilge [EMAIL PROTECTED] wrote:

 Dear all,

 I would be glad to hear what (simple) method I should use to determine
 protein concentrations as accurately as possible. Presently, I'm measuring
 absorption at 280nm with a nanodrop device. I either have 0 or 1 tryptophan
 and no activity test.

 Many thanks in advance!

 Best regards,

 Mark

 Mark Hilge
 Protein Biophysics
 NCMLS 274
 3rd floor M850.03.035
 Geert Grooteplein 28
 6525 GA Nijmegen
 The Netherlands

 http://www.mark-hilge.com

 Phone: 0031 24 36 10 525



 Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het
 handelsregister onder nummer 41055629.
 The Radboud University Nijmegen Medical Centre is listed in the Commercial
 Register of the Chamber of Commerce under file number 41055629.




-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 [EMAIL PROTECTED] [EMAIL PROTECTED]

Re: [ccp4bb] applied optics--LCD projectors

[Jim Fairman]

Pat,

Anandtech is a tech website that does alot of hardware reviews on just about
everything you can think of.  I don't know what your budget is or what
resolution it is you're looking to project but you can get a 1920x1080
projector anywhere from $9000.00 and up.  They may be somewhat pricey, but i
guarantee none of your speakers will complain about bad image quality
again.  I have several suggestions:  Samsung SP-A800 and the Marantz
VP-15S1.  These are just a few out of many many many projectors.

Cheers, Jim

On Wed, Jul 30, 2008 at 5:26 PM, Patrick Loll [EMAIL PROTECTED] wrote:

 This is way off-topic, but that's never stopped me before. And what group
 is better qualified to pontificate about matters lying at the intersection
 of computers and optics than this one?
 The LCD projector in our departmental seminar room was stolen over the
 weekend (!), and I have been asked to look into what we should buy to
 replace it.  The missing projector was a Dell 3300MP, and IMHO it sucked. If
 I had a nickel for every seminar speaker who said, Well, you can't see
 this, but on my laptop it's very clear that..., I'd never need to write
 another grant.

 Alas, I know very little about what's available and what performs well.
 Perhaps you can save me hours of careening around the internet researching
 this question.   Do any of you good folks have experience with particular
 projectors that you like/don't like? Or perhaps have a reasoned opinion (or
 even a wild irrational idée fixe) about the sorts of specifications a good
 projector should exhibit? The room in question is not large (about 8 x 10 m,
 seating a max of ca. 40 people for a talk).

 I should mention that we're NOT looking for any kind of stereographic
 projection here (cool as that would be); just plain, vanilla, projection of
 the image shown on the laptop's screen.

 Many thanks for any info you can contribute.

 Pat


 ---

 Patrick J. Loll, Ph. D.

 Professor of Biochemistry  Molecular Biology

 Director, Biochemistry Graduate Program

 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

 [EMAIL PROTECTED]




-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 [EMAIL PROTECTED] [EMAIL PROTECTED]

Re: [ccp4bb] 3D model building without CRT monitor

[Jim Fairman]

Hello all,

There is a new company around that makes a 3D capable 22 inch flat screen
LCD monitor (http://www.iz3d.com) capable of a maximum resolution of
1680x1050.  It is originally designed for the purpose of playing video games
in 3D, but looks promising for ridding ourselves of the huge bulky CRTs.

Cheers

On Mon, Jun 2, 2008 at 11:08 AM, Warren DeLano [EMAIL PROTECTED] wrote:


 For used-stereo-3D-capable-CRT seekers, our stereo 3D page may be of some
 use.  A number of target monitors are listed.

 http://pymol.sourceforge.net/stereo3d.html

 -Original Message-
 From: CCP4 bulletin board on behalf of Krojer,Tobias
 Sent: Mon 6/2/2008 5:24 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] 3D model building without CRT monitor

 Dear all,

 recently some of our CRT monitors broke down and we realized that these
 monitors are no longer produced. However, we would still like to
 continue model building in 3D which is apparently not possible with
 current TFT displays. Beside the possibility of getting old CRT monitors
 at ebay, I was wondering how other groups solved this problem.

 Thank you very much for suggestions!
 best wishes,
 Tobias




 Tobias Krojer, PhD
 IMP (Research Institute of Molecular Pathology)
 Dr. Bohr-Gasse 7
 1030 Vienna
 Austria
 Tel.: +43-1-797303358
 Fax.: +43-1-7987153





-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 [EMAIL PROTECTED] [EMAIL PROTECTED]