Re: [ccp4bb] vitrification vs freezing

I enjoyed following this thread. Because English is not my first language, I was hoping to learn the official definitions of these terms. In my opinion, all the variations proposed so far are fine - I don't see problems with using them. For me, when I see flash frozen in liquid nitrogen or

Re: [ccp4bb] vitrification vs freezing

I was going to mention that too, but since I was a postdoc of Petsko my words could have been viewed as biased. Quyen On Nov 16, 2012, at 1:26 PM, Ronald E Stenkamp stenk...@u.washington.edu wrote: I'm a little confused. Petsko and others were doing

Re: [ccp4bb] vitrification vs freezing

Hi Ed, If we speak the way scientific articles are written... By Bernard Dixon, published in New Scientist, 11 April 1968, p.73, an imaginary conversation at breakfast: Daddy, I want cornflakes this morning. Must I have porridge? Yes. It has been suggested by mummy that, in view of

Re: [ccp4bb] Deposition of riding H: R-factor is overrated

different models; one precisely reflects the model used in refinement and the other an energy minimized model with predicted hydrogens and alternative conformations removed? Cheers, Quyen __ Quyen Hoang, Ph.D Assistant Professor Department of Biochemistry

Re: [ccp4bb] Deposition of riding H: R-factor is overrated

start a discussion of 'how to resolve' the problems exposed by this thread so far - assuming that you agree that it's a problem worth your time. Cheers, Quyen __ Quyen Hoang, Ph.D Assistant Professor Department of Biochemistry and Molecular Biology, Stark

Re: [ccp4bb] what to do with disordered side chains

___ Quyen Hoang, Ph.D Assistant Professor Department of Biochemistry and Molecular Biology, Stark Neurosciences Research Institute Indiana University School of Medicine 635 Barnhill Drive, Room MS0013D Indianapolis, Indiana 46202-5122 Phone: 317-274-4371 Fax: 317-274-4686 email: qqho

Re: [ccp4bb] what to do with disordered side chains

] On Behalf Of Quyen Hoang Sent: Thursday, March 31, 2011 3:55 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] what to do with disordered side chains We are getting off topic a little bit. Original topic: is it better to not build disordered sidechains or build them and let B-factors take care

Re: [ccp4bb] what to do with disordered side chains

:27:58AM -0400, Quyen Hoang wrote: Thank you for your post, Herman. Since there is no holy bible to provide guidance, perhaps we should hold off the idea of electing a powerful dictator to enforce this? - at least until we all can come to a consensus on how the dictator should dictate

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

Will this affect my reprocessing of the data with D*TREK on my journey to XPLORE the planets MERCURY and rPLUTO in my ENDEAVOUR to find and BUSTER some CRYSTALS with my on-board TNT into XPOWDER? I am still trying to GRASP the idea of AUTODOCKing on precise HKL locations based on the SHARP

Re: [ccp4bb] what to do with disordered side chains

If these users exist (I don't doubt that they do), then they would also might think that lysine residues sometimes look identical to alanine - if the atoms after beta carbon of the lysine are deleted in the PDB due to lack of density. So, I guess, if one's objectives in solving structures are

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

all gitty Cheers, Quyen On Apr 4, 2011, at 5:19 AM, Eleanor Dodson wrote: Very clever.. Eleanor On 04/01/2011 03:19 PM, Quyen Hoang wrote: Will this affect my reprocessing of the data with D*TREK on my journey to XPLORE the planets MERCURY and rPLUTO in my ENDEAVOUR to find and BUSTER some

Re: [ccp4bb] Nanodrop versus Nanophotomter Pearl versus good old Bradford.

We also have not experienced any problems with a Nanodrop 2000C. No one in my touched the two boxes of Bradford and BCA kits that we have, because we have been very happy with the Nanodrop. Quyen ___ Quyen Hoang, Ph.D Assistant Professor Department of Biochemistry

Re: [ccp4bb] should the final model be refined against full datset

Sorry, I don't quite understand your reasoning for how the structure is rendered useless if one refined it with all data. Would your argument also apply to all the structures that were refined before R-free existed? Quyen You should enter the statistics for the model and data that you

Re: [ccp4bb] should the final model be refined against full datset

at 1:20 PM, Quyen Hoang qqho...@gmail.com wrote: Sorry, I don't quite understand your reasoning for how the structure is rendered useless if one refined it with all data. Useless was too strong a word (it's Friday, sorry). I guess simulated annealing can address the model-bias issue

Re: [ccp4bb] should the final model be refined against full datset

: On Fri, Oct 14, 2011 at 1:20 PM, Quyen Hoang qqho...@gmail.com mailto:qqho...@gmail.com wrote: Sorry, I don't quite understand your reasoning for how the structure is rendered useless if one refined it with all data. Useless was too strong a word (it's Friday, sorry). I guess simulated

[ccp4bb] Postdoctoral Position in Structure Biology of Neurodegenerative Disease

Postdoctoral position available: A postdoctoral position is available to study the mechanisms of Parkinson disease. Genetic studies in the past decade have identified a number of genes as causal factors of Parkinson disease. Our goals are to understand the biochemical and biological

Re: [ccp4bb] sulfur sad phasing

___ Quyen Hoang, Ph.D Department of Biochemistry and Molecular Biology, Start Neurosciences Research Institute Indiana University School of Medicine 635 Barnhill Drive, Room MS0013D Indianapolis, Indiana 46202-5122 Phone: 317-274-4371 Fax: 317-274-4686 email: qqho...@iupui.edu On Nov 11

[ccp4bb] Postdoc Position in Molecular Neuroscience

interest in science and desire to learn new techniques to tackle challenging and important questions. Please email a cover letter, CV, and three reference letters to: qqho...@iupui.edu Thank you for looking and happy holidays! Cheers, Quyen ___ Quyen Hoang, Ph.D

[ccp4bb] Postdoctoral Positions Available

Postdoctoral Positions at Indiana University School of Medicine My lab will have two postdoc positions available, one immediately and the other in April 2015. A summary of what we do can be found at http://snri.iusm.iu.edu/people/primary-investigators/quyen-q-hoang-ph-d/

Re: [ccp4bb] Off topic - Mercury Lamp for Akta

We buy UV lamps from Jelight Company Inc. for replacements on our AKTA systems (http://www.jelight.com/low-pressure-uv-lamps.html http://www.jelight.com/low-pressure-uv-lamps.html). It’s not a direct replacement in that a few modifications needed to be made: 1. cut two groves on the lamp base

[ccp4bb] Postdoctoral position in structural biology of neurodegeneration

of research interests and career goals, CV, and contact information for three references to Dr. Quyen Hoang (qqho...@iu.edu). Cheers, Quyen Quyen Hoang, PhD Associate Professor of Biochemistry and Molecular Biology Adjunct Associate Professor of Neurology Primary Investigator of the Stark

Re: [ccp4bb] Optimisation of 2D very thin plates to thick plates

revealed that it was actually P21. Hope this helps. Cheers, Quyen Quyen Hoang, PhD Associate Professor of Biochemistry and Molecular Biology Adjunct Associate Professor of Neurology Primary Investigator of the Stark Neuroscience Research Institute Indiana University School of Medicine 635 Barnhill

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

I guess that one might need a way to avoid natural mutations that could turn B into B’ or B". Quyen Quyen Hoang, PhD Associate Professor of Biochemistry and Molecular Biology Adjunct Associate Professor of Neurology Primary Investigator of the Stark Neuroscience Research Institute In

[ccp4bb] Postdoc positions

...@iu.edu) if you are interested in learning more about these positions. Cheers, Quyen ___ Quyen Hoang, PhD Associate Professor of Biochemistry and Molecular Biology Director of IUSM Center for Electron Microscopy (iCEM) Adjunct Associate Professor of Neurology Primary Investigator of the Stark

Re: [ccp4bb] To Trim or Not to To Trim

no talk. Cheers, Quyen Quyen Hoang, PhD Professor of Biochemistry and Molecular Biology Director of IUSM Center for Electron Microscopy (iCEM) Adjunct Professor of Neurology Primary Investigator of the Stark Neuroscience Research Institute Indiana University School of Medicine 635

Re: [ccp4bb] To Trim or Not to To Trim

Hi Debanu,In your example, I would guess that models with truncated side chains would probably be problematic too, so would alternative conformations, unmodelled segments, asymmetric unit consisting of only a fraction of the biological/functional unit, etc.I am not sure if it is possible to build

[ccp4bb] Structure prediction - waiting to happen

ime, I decided to learn how to solve the structure to proof > my prediction is correct. Now, it is interesting to see now the question is > on the other side.  > > River > > From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Quyen Hoang > Sent: Sunday,

Re: [ccp4bb] [External] Re: [ccp4bb] Structure prediction - waiting to happen

Thank you for having this conversion. I have heard this question more than once (why is experimental determination needed when there is Alphafold) at grant study sections. Some came from structural biologists, so hopefully, the discussion here would help them also. Computational modeling had

[ccp4bb] Technician Position available

(qqho...@iu.edu). Cheers, Quyen __ Quyen Hoang, PhD Professor of Biochemistry and Molecular Biology Director of IUSM Center for Electron Microscopy (iCEM) Adjunct Professor of Neurology Primary Investigator of the Stark Neuroscience Research Institute Indiana University School of Medicine 635