tag:blogger.com,1999:blog-54333942011-11-30T11:37:48.416-08:00Access to SpaceA dialog about NASA Programs , Biotechnology, and the Futurexcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.comBlogger551100tag:blogger.com,1999:blog-5433394.post-80691769048908392022011-10-24T11:35:00.000-07:002011-11-30T11:37:48.431-08:00PH domains in ROCKWe are looking at interactions of ROCK's catalytic domain and ROCK's PH domain. Interesting to look at a range of PH domains from many proteins. Here is a structural alignment done in VMD.xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-54165127910980579492011-04-23T23:26:00.000-07:002011-05-19T23:36:20.301-07:00CrystalsI have set up and am getting some initial leads for the Hampton screening tray that I am using. I have also set up co-crystals with an inhibitor. I am using my digital camera and the microscope to capture images during crystal growth.xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-64151014631039596962011-02-22T16:49:00.000-08:002011-02-22T17:20:53.672-08:00More ProteinWell I pressed ahead and cultured 7 liters of my protein. We use a arabanose induced chaperone before we induce with IPTG to help folding. After harvesting I placed in a Ni resin, because we have a His tag. In all I finished around 5:30 am. I was able to get home, get a hour cat nap, shower, and get back for a meeting. ... What an all nighter. Though all researchers know this is par xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com1tag:blogger.com,1999:blog-5433394.post-24006496975451147712011-02-17T11:04:00.001-08:002011-02-17T11:21:22.751-08:00Frontiers in Translational MedicineI have been enjoying the keynote addresses today it what is the "Inaugural Scientific Symposium for The Methodist Hospital Research Institute". I learned important information about mechanisms is cancer from the first speaker, Michael Kastan. I was very interested in his results from the compound CP466722... It has provoked the need for more reading of his xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1499007194760631692011-01-14T22:37:00.000-08:002011-01-14T22:38:37.310-08:00INSTALLING NMRDRAWWell, the installation failed at first because the com and nmrtxt directories were not correctly unpacking from the NMRPipeX.tZ file correctly. I looked into the install.com script and noticed the line:cat $srcDir/NMRPipeX.tZ | zcat | tar xvf - >>& tar.logwhich allowed me to test the individual steps to isolate the problem.After numerous tries, I eliminated all the lines in my xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-74969410582456541722010-12-09T17:58:00.000-08:002011-01-09T17:59:35.640-08:00Binding RocksBiacore experiments on our protein has demonstrated binding to its subdomain. Its binding was very tight and we need to verify the phosphorylation state of the protein as we have hypothesized that binding is dependent on its state.xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-91165702488169916882010-09-23T18:10:00.000-07:002011-01-09T18:11:26.795-08:00 Unix Rebuild1) Rebuilding Cybermen i) After a number of tries, the boot and data disks are now working 2) Rebuilding Fedora on Vandusen i) is basically working ii) ssh to a remote machine works (ie super computers cluster) iii) remote login local does not? Port 22 refused?xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-7334896990246786612010-03-10T18:02:00.000-08:002011-01-09T18:03:24.600-08:00Filter Order Omega OpticalWe have updated our Tecan fluorescence plate reader390BP10490BP10 465BP35535BP25xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-85652509130836651052010-02-19T13:00:00.000-08:002010-02-19T13:24:48.700-08:00A New Beginning in Structural BiologyThe University of Houston has been very fortunate to recruit a number of top scientists in the Department of Biology and Biochemistry and the Department of Chemistry. First, Dr. Scott Gilberston (home page home page) came, bring an expert research knowledge in synthetic chemistry for peptiomedics. Then the university was able to bring Dr. Schwartz (home page)xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-49783781407180439362009-10-15T08:44:00.000-07:002009-10-15T08:48:10.297-07:0044th US Japanese Conference on Cholera and Enteric InfectionsWe have an excellent conference in San Diego on Cholera and other enteric infections. We had a chance to talk to many people in the field and get feedback on our research.xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-31713157841452818632009-06-30T09:42:00.000-07:002009-06-30T09:45:10.280-07:00Energy LandscapesWell I have finished a set of CHARMM preparations for a mapping the transition pathways and the energy landscapes along those trajectories for the activation of LFA-1 I-domain. Now moving the topology files and pdb files to the Atlantis computing cluster.xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-60388018226002445522009-05-16T15:59:00.000-07:002009-07-16T15:59:59.268-07:00Check out GraduationGraduationxcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-19750142453156041872008-12-30T14:05:00.000-08:002008-12-30T14:42:29.179-08:00Running DynamicsWe have started a new dynamics simulation on another machine because our Itanium2 cluster has been core dumping NAMD. Why, I do not know? The error message is "regcache incompatible with malloc", though I am not sure why we got this message. Also, I have had this message on runs that worked. This new machine is a SGI Altix and we will see if job 3732 runs to completion.xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-80680187130998184822008-12-15T15:53:00.000-08:002008-12-15T16:00:38.785-08:00Isotope Filter Pulse ProgramsWell I have finished the paper before Thanksgiving so now am expanding the documentation for my thesis. Hoping to get some good graphic program to make diagrams for a presentation I will give. In the past, I have used postscript edited by hand. The spectra for the paper and thesis look great this way! Anyway, I will evaluate any postscript editors I can get my handsxcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-57778042500106558542008-07-24T17:52:00.000-07:002008-07-24T17:57:25.592-07:00CharmmWe are getting Charmm and NAMD setup with our favorite protein. Actually this was initially done last year but I am getting John to finish the project because I have not had the time. The build, solvation, and first minimization ran today.JWCxcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-23287480148021453172008-07-15T12:04:00.001-07:002008-07-16T09:33:19.525-07:00A Modified Nuclear Magnetic Resonse Pulse Program for Our Bruker 800Well, I have had the chance to get into some pulse programming because a NOESY-HQSC experiment that we need required the 3D program to be modified to a 2D version. The 1H / 13C correlation for this experiment is through a double inept transfer with 13C (and 15N) filter in the F1 dimension. The primary change in the pulse programxcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-70505171951686663412008-06-18T07:23:00.000-07:002008-06-18T07:29:33.715-07:00Cool testingxcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-56098750463443530002008-05-01T15:56:00.001-07:002008-05-01T15:56:45.083-07:00DarfurThe holocaust museum had a excellent speakercome and talk about Darfur and what common people can do to make a difference in the crisis. As the conflict begins to spill over into Chad and the Central Republic, we need to stay involved in pushing our elected officials to apply pressure on the Sudanese government. At the University of Houston, we are planning a walk to help raise awareness xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-13404690409506391142007-11-24T12:08:00.000-08:002008-02-15T12:09:04.016-08:00The Welch ConferenceI felt that the Welch Conference in October was one of the best I have been to. It was titled Physical Biology – From Atoms to Cells, and it covered many topics including folding, novel amino acids, membranes, and quantum physics. The key note speakers were the Welch awardees, Noel Hush and William Miller. However the conference also featured many Noel Prize winners.The xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-49004986067921787892007-09-10T17:59:00.000-07:002007-10-31T18:00:38.469-07:00Dr. James Watson's Contradicting Statements on EthicsI greatly appreciate the efforts that the Houston Holocaust Museum has done putting on the lecture series "Science and Medicine: After the Holocaust". Both the speakers, Dr. James Watson and Dr. Eric Kandel, were great. But for me the most interesting thing in the lecture was Watson's notion of "good" genes and "bad" genes and that somehow "xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com1tag:blogger.com,1999:blog-5433394.post-43596173875626411342007-08-01T00:01:00.000-07:002007-08-01T00:02:57.725-07:00HELP on NERO Install in Linux!Real Question: How do you install a later version library required by a new tool (nero)on your old version of linux ( uname -r 2.4.20-31.9 ) without breaking the older programs.Tried to install Nerorpm -i nerolinux-3.0.0.0b-x86.rpmerror: Failed dependencies: glib2 >= 2.4.7 is needed by nerolinux-3.0.0.0-1 gtk2 >= 2.4.10 is needed by nerolinux-3.0.0.0-xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-74280872335394221722007-06-24T17:48:00.000-07:002008-12-06T07:16:08.277-08:00Fixing the 800The Bruker tech guys came by to upgrade our version of xwinnmr to topspin because of some new feature that would help with our D2O lock... anyway, by the time they got that done something in the new software misconfigured information that probably led to the burnout of a resistor on the Shim-Lock-Control Board. Then the shim stack became suspect. Before we knew it we had to warm xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-29782059946002722582007-06-02T22:38:00.000-07:002007-06-02T22:39:25.520-07:00Update to templateDear viewer,I have updated the template because Blogger changed the location of my archive files. It should now work.JWCxcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-15153228487396227952007-05-28T07:33:00.001-07:002007-05-28T07:55:52.714-07:00Biophysics BonanzaI have enjoyed helping Dr. Legge prepare lecture materials for the Biophysics couse. You can go check out the syllabus out at the coursepage. We covered a lot of material and all of that material was prepared fresh this semester. Dr. Gray, who had been the professor who taught this class before, had retired and Dr. Legge focused the class more on spectroscopy rather then xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-78301536939710901102006-09-27T17:21:00.000-07:002007-03-17T17:21:40.527-07:00Fly with the BirdsWhile at Scripps, we also stopped by the NMR facility. They of course have an impressive array of Bruker NMR spectrometers, including a 900 Megahertz instrument. The manager is Dr. Croon, who I found out enjoys ornithology. One thing that I could share with Dr. Croon is an excellent birding site called High Island on the Bolivar peninsula along the Gulf of Mexico. I have xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-72290720775881129082006-09-26T07:52:00.000-07:002007-03-17T07:58:34.855-07:00NMR Transcends Human LanguagesAfter the Protein Society meeting Dr. Legge and I went to visit his old stomping grounds, the Peter Wright Lab at Scripps. Chiaki Nishimura, a long time postdoc in the lab, has been doing some interesting dynamics as described in his recent paper. As Dr. Legge and Chiaki caught up, I noticed the abundance of NMR materials in Japanese (behind the Enchilosa soup!). Thexcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com1tag:blogger.com,1999:blog-5433394.post-1149064971681599492006-05-20T19:42:00.000-07:002006-05-31T01:42:51.710-07:00UTMB Structural Biology SymposiumThe University of Texas Medical Branch at Galveston (UTMB) eleventh Structural Biology Symposium is here again and the keynote speaker, Alan Fersht, spoke about protein stability issues in the context of evaluating the melting points of P53 and the possibility of using small peptides to stabilize the protein. However, I found Jacqueline Barton's talk on the xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com1tag:blogger.com,1999:blog-5433394.post-1145736348829015042006-04-22T13:05:00.000-07:002006-04-22T13:05:48.840-07:00Innovations in Nanoscale Modeling and Imaging of Biological Systems.We are wrapping up this workshop today with an interesting talk from Masahide Kikkawa and others on Helical Reconstruction. This followed many talks image filtering and model fitting. Many software packages including Situs by Dr. Wriggers and Signature by Dr. James Chen were presented. One of my favorite points of discussion xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1139920283395731462006-02-14T04:31:00.000-08:002006-02-14T04:31:23.406-08:00Ready to Look at an Old SampleWell early this morning I was able to get on the Bruker 600 and set up my sample. The temperature was set via edte to 293K and the lock looks good on this sample. Last week I had some difficulty locking (h20/d20) a sample with a small volume (I had a low concentration so wanted to minimize the volume). This sample lock right away and the tune and match procedure (xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1130870561635972702005-11-01T10:42:00.000-08:002005-11-01T10:42:41.646-08:00That cursed hidden character!Don't you hate it when you have a file that clearly looks right and yet you seem to still get some vague error message (if you are lucky) The classic problem I have is using TAB's instead of SPACE's for picky programs or compilers. The editor that I swear by is vi. It is on ever unix machine and always works. So I use :set list to see those elusive characters. Ifxcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1129335325737896142005-10-14T17:06:00.000-07:002005-10-14T17:15:25.736-07:00Published!Well my first paper has been published in the Journal of Biomolecular NMR this September 2005. It has an ISSN: 0925-2738 number and a title as "An AMBER/DYANA/MOLMOL Phosphorylated Amino Acid Library Set and Incorporation into NMR Structure Calculations". You can go to PubMed and query "Craft NMR" and the abstract will pop up. The exciting thing is that we have the science that thesexcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1128181293821544002005-09-22T08:40:00.000-07:002005-10-01T08:41:35.306-07:00Collecting SpectraDr. Legge and I have been working on a protein structure. Here we are using the Bruker 800 MHz and collecting spectra for the protein structure. We worked late to get the experiment on before I had to leave and pack for Rita.xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1125388745010318872005-08-30T00:58:00.000-07:002005-08-30T00:59:05.016-07:00MOLMOL Library Broken Link FixedTo everyone that tried to download the link: http://www.bchs.uh.edu/~glegge/phospho_lib/lib/amber94.lib from the website, I am sorry that link from the installation guide for the phosphoresidue libraries was broken. It has been brought to my attention and now I have updated the file.Thanks, and as always please send requests to jjwwcraft@yahoo.com or jwcraft@xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1119846153896880042005-06-26T21:22:00.000-07:002005-06-26T21:23:40.320-07:00Bruker 600 Mehmet and I have been working on a short 19 amino acid residue polypeptide. Here we are using the Bruker 600 MHz and collecting spectra for the peptide structure.xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1118825631406642622005-06-15T01:46:00.000-07:002005-06-15T01:53:51.413-07:00AMBER LibrariesI now am testing a web page layout to download the phospho_lib tar files. Right now I have a mirror on my blogger space (http://members.aol.com/jjwwcraft/phospho_lib/index.html), and I am building a version for the UH web server. Hopefully I can polish the pages and text so that I can close out this project and make the libraries and MATLAB script available to the user community.xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1117204602097522872005-05-21T07:36:00.000-07:002009-07-16T15:51:30.377-07:00UTMB Structural Biology Symposium Features Dr. Karplus as Keynote SpeakerThis years structure biology symposium held at the University of Texas Medical Branch in Galveston Texas was kicked off by a talk from Dr. Martin Karplus. Dr. Karplus is famous for many things, the one in which I am most familiar is the Karplus equation, J=A+Bcos(dihedral)+Ccos2(dihedral) for J-coupling in NMR spectroscopy.xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1117204510833744192005-05-17T07:33:00.000-07:002009-07-16T16:05:44.410-07:00Sigma XiBoth Mehmet and I presented posters at the Sigma Xi poster competition.xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1117203516269624212005-05-13T07:18:00.000-07:002009-07-16T16:06:13.433-07:00Swish, The Semester is Gone!Wow, I have hardly written an entry over the last two semesters, and I can barely catch my breath, .... but today is the last day of the semester. There is a lot of catching up, if you have been following my blog (probably it is not on you short cuts lists anymore, as there have been so few updates). but I will try to give some highlights over the next few days. xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1114228197860879002005-04-22T20:48:00.000-07:002005-04-22T20:53:43.683-07:00Symphonic WindsOne of the great things about the University of Houston is its diversity. Diversity of people, their backgrounds, and their aspirations. This is clearly reflected in the wide number of degree areas sought here. One seemingly hidden area of excellence on campus is in the talents brought to life in the Moores Opera House, where tonight a stellar performance of music that would xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1098250058325917012004-10-19T23:27:00.000-07:002004-10-19T22:29:12.136-07:00Now Starting on Phospho-Threonine
I finished the phospho-Serine a couple of weeks ago and ran both DYANA and AMBER with the parameters. Now I am starting on the phospho-Threonine that we will soon need. On a parallel track I am excited that my son Jacob has just arrived. I plan to be back in the lab ASAP, but I need to enjoy this moment.
xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1096033351025187722004-09-24T06:37:00.000-07:002004-09-24T06:42:31.026-07:00AMBER LIBRARIES
I have been foiled in my attempt to build a phosphoserine library for AMBER despite the fact that I know that others seems to have done it. Could anyone comment one my strategy to build this library? I am sure I am close, but ... you know how working with code that you are just learning goes.... anyway I would also like to know the relationships between the many library files xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1094054147943043682004-09-01T08:51:00.000-07:002004-09-01T08:55:47.943-07:00Using the HSG Convention in tLeap / Amber
I have updated the leaprc.ff99 file so that the nomenclature of HSG and HG is mapped for the amino acid residue cysteine. This was done using the addPdbAtomMap command as shown below.
I am using .../dat/leap/lib/all_aminont02.lib and it has these lines:
!entry.NCYS.unit.atoms table str name str type int typex int resx int flags int seq int elmntxcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1093623976710613832004-08-27T09:25:00.000-07:002004-08-27T09:26:16.710-07:00Protonate
I developed the automation script after getting one successful dyana->leap->sander run completed. It should have worked correctly, however the same error occurred. FATAL: Atom .R NCYS 1.A HS 14 does not have a type. I have now discovered that I had correctly modified the nomenclature for the cysteine residue's proton on the sulfur atom. I had in fact used HSG as required. That xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com1tag:blogger.com,1999:blog-5433394.post-1093573945515488092004-08-26T19:31:00.000-07:002004-08-26T19:32:25.516-07:00Using AMBER for Molecular Dynamics
I have a peptide tail that has a CYS residue as the n-terminous and when I run tleap:
tleap -s -f leaprc.ff99.tf using what I thought was the correct pdb syntax file
...
ATOM 1 N CYS 1 1.325 0.000 0.000
ATOM 2 H1 CYS 1 0.858 -0.893 0.114
ATOM 3 H2 CYS 1 1.960 0.150 0.776
ATOM 4 H3 CYSxcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com1tag:blogger.com,1999:blog-5433394.post-1092762972493897662004-08-17T10:10:00.000-07:002004-08-17T10:16:12.493-07:00Using AMBER
Well I have gotten AMBER running on one of our machines. The next key task is to get it running on a cluster of SGI's using a batch submit script. The version I got running is on an Onyx and takes a fair amount of time to run. We have got to get the performance better.
#Processors | Time
------------------------------
1 | 11 minutes / run
2 | 7.5 minutes / runxcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1085238953900168832004-05-22T08:15:00.000-07:002004-05-22T08:15:53.900-07:00Correlation between TOC and NOE Data
One of the problems of the two dimensional Nuclear Magnetic Resonance (NMR) data that I am looking at this morning is that a significant number of peak contours are convoluted between multiple peaks. I have been able to use the correlation of peak data between Nuclear Overhauser Effect (NOE) and TOtal Correlation SpectroscopY (TOCSY) contours to discriminatexcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1082752361155012492004-04-23T13:32:00.000-07:002004-04-23T13:35:41.390-07:00Nuclear Overhauser Effect (NOE) Links to Neighboring Residues
The chemical shift values for the unphosphorylated tissue factor cytoplasmic tail provides good insight and confirmation of the amino acid sequence. The major classification of the spin systems was completed using the TOC peaks and collaborated by inphase homonuclear 2D correlated spectroscopy (IP_COSY) experimental data. The TOC xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1078383742729757582004-03-03T23:01:00.000-08:002004-03-03T23:04:32.606-08:00Buffer Preparations
(notes 3/3/04 jwc)
The main task today was the preparations of three buffers for the protein purification step. The homogeneity buffer was:
1) 25 mM HEPES
2) 0.1mM EDTA
3) 0.5 M NaCl
As 200 ml was required, 1.192 grams of Hepes, a dilution of .5 M EDTA stock using 400 microliters, and 5.844 gram of NaCl were prepared in about 130 ml of double deionized water chilled at 4 xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1077913692188664112004-02-27T12:27:00.000-08:002004-02-27T12:30:16.623-08:00MOLMOL - MOLecule analysis and MOLecule display
I have been trying to get molmol to work on my Mac using the X11 Darwin interface. The basic program works fine, but all the dialog boxes come up as small (a few pixels) windows without resize handles. If anyone out there knows how to fix this please email me at xcrabturtle@yahoo.com. I have posted a question on the email list too. Anyway, one xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1071247834123727662003-12-12T08:49:00.000-08:002003-12-12T08:51:21.110-08:00Getting the Inertia Tensor Right!
Jay Estes, a friend of mine has done a great job making the explanation of how to use the inertia tensor in your equations of motion. The key is to remember that inertias are often calculated and reported in the structural frame. However, you often compute dynamics in a body frame. The X38 example below show the typical situation that needs to be accounted forxcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1071247725008932822003-12-12T08:47:00.000-08:002003-12-12T08:49:32.013-08:00Maybe a Better Vector Formulation of EOM
As is often the case, using matrix math simplifies the notation for engineering problems. Here I have solved from the angular accelerations from the moment equation in closed form. This equation can now be implemented directly in a program like Matlab and solved using ode45. ode45 is the ordinary differential equation routine provided in Matlab.
xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1070207857436511122003-11-30T07:51:00.000-08:002003-11-30T07:58:13.293-08:00Cross Products
Often a cross product is required in the application of dynamics of the equation of motions. This is especially true for the moment equations and their relationship to the angular rates.
I always preferred to follow the first form because I never need to remember the sign conventions. However in the next section on determinants it will be seen that the signs are laid out inxcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1070148803852536772003-11-29T15:32:00.000-08:002003-11-29T15:33:58.560-08:00Principles for Building a Simple 3DOF Simulation
Remember to begin with Newton's laws.
First: a body at rest or moving straight will remain at rest or move straight if no unbalanced force is applied.
Second: A particle acted on by a force F has an acceleration a in the same direction and proportion to the force F.
Third: For every force acting on a particle, the particle exerts an equal xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1054305325189655782003-05-30T07:35:00.000-07:002003-05-30T07:35:25.040-07:00Importance of X38 Technologies
Few Americans know the significant advances and cost effective capabilities developed by NASAs X38 program. That program has been a victim of the cost cutting requirements of Sean OKeefs administration. No one doubts the need for cost improvement and program consolidation. This was especially true for the parallel programs of Crew Rescue Vehicle (CRV) and Crew xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0tag:blogger.com,1999:blog-5433394.post-1054129581870025602003-05-28T06:46:00.000-07:002003-05-28T07:29:54.206-07:00My Mission Statement
1) Provide a dialog for improvements in Access to Space
2) Provide helpful Mac OSX hints
3) Provide explanation of configuration control
4) Provide HTML generator for source code documentation
5) Provide Java based Go and Connect 4 Games
My goal is to promote a dialog about space policy and review many of the programmatic problems that an agency like NASA faces. NASA is a xcrabturtlehttp://www.blogger.com/profile/11711066001266944496noreply@blogger.com0