atest" 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:
&g
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
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&item=ryzen-linux-10way&num=3
----------
Jim Fairman
C: 1
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 li
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:
> De
sewhere as well:
http://accessories.dell.com/sna/productdetail.aspx?c=us&l=en&s=fed&cs=16&sku=A7035595
I can vouch for the VG248QE monitors working with 3D Vision 2, I have 2 of
them.
Cheers, Jim
----------
Jim Fairman
s 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
eautifully.
------
Jim Fairman
C: 1-240-479-6575
On Tue, Nov 28, 2017 at 6:40 AM, mesters
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 N
s, Jim
------
Jim Fairman
C: 1-240-479-6575
On Thu, Nov 17, 2016 at 12:40 PM, Wei Wang 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.
>
> Ano
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, Ju
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
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
t 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 Chemi
der 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
gt;
> 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
ly 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 <htt
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
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
rial 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
&g
--
> ***
>
> Jacob Pearson Keller, PhD
>
> Looger Lab/HHMI Janelia Farms Research Campus
>
> 19700 Helix Dr, Ashburn, VA 20147
>
> email: kell...@janelia.hhmi.org
>
> ***
>
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
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/>
EE1A
>
> -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--
usion 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
gt; 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: 206-780-89
aratus 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
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
>
-
-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
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
You can do structure based sequence alignments using STRAP. It's java based
and free.
On Aug 18, 2011 5:20 AM, "Suda Ravindran" 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.
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.
Po
e 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.go
Molecular Biology,
> but do
> not know how to make a stereo image of electron densities as required by
> the
> journal. We would appreciate it very much if you give us some detailed
> protocols
> on doing that.
>
> Thanks!
> Matt
>
--
Jim Fairman, Ph D.
Post-Doctor
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" wrote:
> Nvidia lists that monitor on their list of supported hardware:
> http://www.nvidia.com/object/3d-vision-requirements.html
>
> They even sell some Ace
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 t
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
> 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: &l
:
> 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 -
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 wrote:
> Stereoscopic 3D driven by OpenGL via an Nvidi
rrive 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
ly 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-Ketterin
>
> 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
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
r 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
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
bright red band of pigment is present in the pellet. Has anyone experienced
this red pigmentation before while using this strain (or perhaps know what
the pigment might be)? When grown in LB or TB media the same cells show no
pigmentation.
--
Jim Fairman, Ph D.
Post-Doctoral Fellow
National
iversität 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
search 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
uate 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
t 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-
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
t;>> No rights associated with the movie, and the Strasbourg group intends to
>>> release a higher quality version on DVD soon. Please contact them about
>>> that... I am only sharing what I thought was good for educational purposes.
>>> 18 minutes of your life, but
gt;> 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
earch - 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
f 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
ng 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
>
>
>
> C
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
gt; 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
> > D
ligomer. 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
--
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
nclusion 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 Ass
o 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.
>>
t 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
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 Unive
> 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]
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]
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
gt; 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
Gradua
> ---
>
> Patrick J. Loll, Ph. D.
>
> Professor of Biochemistry & Molecular Biology
>
> Director, Biochemistry Graduate Program
>
> Drexel University College of Medicine
>
> Room 10-102 N
gt;
> 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
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