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:
> Hi
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=ryzen-linux-10way=3
--
Jim Fairman
C: 1-240-479-6575
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
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
re 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, De
.
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
.
--
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 u
s, 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 i
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,
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
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
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
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
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
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
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
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
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
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
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
/
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
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
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
,
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
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
--
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
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 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
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
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
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
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
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
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
:
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
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
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
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
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
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
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
--
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
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
/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
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
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
, 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
.
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
but with little success.
--
Jim Fairman
Postdoctoral Research Assistant
Case Western Reserve University
216-368-3337 jxf...@case.edu
.
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
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
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
, 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
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
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
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
.
--
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
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]
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
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]
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
(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
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