Re: [ccp4bb] on space group

Take Care, Sean Seaver, PhD P212121 http://store.p212121.com/ -- Dear All, Alhough there are on-line explainations on the space group, I found it was difficult to fully understand. Here we take P 1 21 1 as an exmaple, will you please explain to me with easy language what each number

Re: [ccp4bb] capillary counterdiffusion agarose plug

Hi Georg, I haven't used the agarose method, but have sealed many capillaries using bees wax without an issue. Simply heat the wax until it melts, dip the capillary (rotate if it has a larger diameter) then let cool. I hope that helps, cheers! Sean Seaver, PhD P212121 http://store.p2

Re: [ccp4bb] Monodihydrosterculin

Hi Pius, I just checked Monodihydrosterculin against our database of more than 1 million antibodies and we aren't seeing anyone that normally offers this product for sale. Take Care, Sean Seaver, PhD P212121 http://store.p212121.com/

[ccp4bb] Traveling Salesman with Simulated Annealing

ealing-r-and-shiny/ Take Care, Sean Seaver, PhD P212121 http://store.p212121.com/

[ccp4bb] Part-time Work for Graduate Students

supp...@p21221.com . Take Care, Sean Seaver, PhD P212121 http://store.p212121.com/

Re: [ccp4bb] Protein-DNA crystallisation

that helps in getting you started, take care! Sean Seaver P212121 http://store.p212121.com/

Re: [ccp4bb] What to put on Custom Declaration for shipped samples?

sizes can be more tightly regulated. Regards, Sean Seaver, PhD P212121 http://store.p212121.com/

Re: [ccp4bb] off topic: a Python online course and others

I'd also recommend: Learn Python The Hard Way By Zed A. Shaw http://learnpythonthehardway.org/ Online Python Tutor http://pythontutor.com/ Take Care, Sean Seaver, PhD P212121 http://store.p212121.com/

Re: [ccp4bb] mosaicity and SAD

atoms Take Care, Sean Seaver P212121 http://store.p212121.com/

Re: [ccp4bb] TCEP resistant disulfide

tion with DTT but >can be reduced with TCEP? This could be due to the effective pH of TCEP HCl (~1.5-8.5) being wider than DTT ~7. Take Care, Sean Seaver P212121 http://store.p212121.com/

Re: [ccp4bb] ShelXL and Coot

Dear Badsha, Is it possible to share the pdb such as by linking to it using dropbox, google docs, etc..? It's hard to trouble shoot the issue without seeing the file. Thanks, Sean P212121 http://store.p212121.com/

Re: [ccp4bb] recombinant enterokinase

, Sean Seaver P212121 http://store.p212121.com/

Re: [ccp4bb] Freezing crystal

blends. DMSO: http://www.bio.brandeis.edu/publications/bi035849h.pdf Sodium malonate: http://journals.iucr.org/d/issues/2003/12/00/fw5004/fw5004.pdf Take Care, Sean Seaver P212121 http://store.p212121.com/

Re: [ccp4bb] Off-topic: ELNs

for a 'free' alternative would consider using google sites ( https://sites.google.com/ ) to roll your own solution. I hope that helps. Take Care, Sean Seaver P212121 http://store.p212121.com/

Re: [ccp4bb] odd arginines

Hi Jacob, A couple of years ago, I put together a list of papers that touch on radiation damage: http://www.p212121.com/2009/11/17/ultimate-list-on-cryocrystallography-radiation-damage/ To answer your question more directly - see pg. 40 of the following paper: http://www.px.nsls.bnl.gov/course

Re: [ccp4bb] Neutron data collection

iquid nitrogen. I hope that helps. Take Care, Sean Seaver P212121 http://store.p212121.com/

Re: [ccp4bb] Mac OSX 10.7 Lion

more screen real estate. Take Care, Sean Seaver P212121 http://store.p212121.com/

Re: [ccp4bb] Sodium ion vs. Water

Hi Jacob, Darn that site doesn't seem to be working. I generated the files ion files and thought it was good to go, but didn't view the outputs. Apologies, Sean Seaver P212121 http://store.p212121.com/

Re: [ccp4bb] Sodium ion vs. Water

Hi Christina, The WASP server seems to working at this location (about half way down the page): http://www.jcsg.org/prod/scripts/validation/sv2.cgi I hope that helps. Take Care, Sean P212121 http://store.p212121.com/

Re: [ccp4bb] Fab:antigen complex crystallization!!!

Dear Ivan, If you take a look at the MPCD ( http://www.cinam.univ-mrs.fr/mpcd/ ) and search for Fab it brings up 172 crystallization conditions. The names should help you narrow down, which conditions are of a complex. Hopefully, you can use those conditions to help you decide, which directio

Re: [ccp4bb] non-waters among structured solvent atoms

>Better yet, RbBr? and pH MES, MOPS, and HEPES with RbOH? >I haven't checked the price. Including shipping in the US RbBr: 50 g 99% pure is ~$150. RbOH: 25g 99+% pure in 50 % water runs about ~$120. It would be interesting to see how the substitution would influence the crystallization or cryst

Re: [ccp4bb] MS sequencing of Fab

>do not diffract to sufficiently high resolution so as to allow us to read off >the sequence from the map). >Since we have access to a lot of pure protein, I wonder if some clever mass >spec jock would be able to assemble >enough overlapping sequenced fragments so >as to give complete coverage

Re: [ccp4bb] Question about movie making

Dear Mark, I put together a post about creating a movie using PyMOL, eMovie (free) and Adobe ImageReady CS2 to generate a Quicktime movie. http://www.p212121.com/2009/03/24/easily-make-movie-pymol/ I hope that helps. Take Care, Sean P212121 http://store.p212121.com/

Re: [ccp4bb] CCP4 for iphones

I've been curious if there has been discussion about moving data processing and refinement to a software as a service (SaaS) deployment. If programs were web accessible then it may save researchers time and trouble (maintaining and installing software). In turn, one could then process data via

Re: [ccp4bb] off-topic: Discovery Studio software

Hi Padmaja, -Will it work on a Mac OS? No -Is there another program (free or cheaper) that will do everything DS does? Currently, there is a free version that you can use of DS. http://accelrys.com/products/discovery-studio/visualization-download.php Hopefully that will give you a feeling if the

Re: [ccp4bb] sodium vs water near methionine sulfur

Hi Chandan, The closest sodium-sulfur interaction that I know of within a protein is in entry 2BDG, Na (Atom 402, Chain A) to a CYS with a distance of 3.3 Angstroms. A couple of examples exist of sodium-sulfur interactions that involve coenzyme A (1FY7 and 1MJ9). I hope that helps. Take Care

Re: [ccp4bb] how to generate density map of selected residues

Hi Michael, The carve command displays the radial density of a selected atom. As per the example, a carve=1.6 would mean that density around a selected atom will be shown with a 1.6 Angstrom radius. The carve command can prove useful in figures in which density obscures relevant information.

Re: [ccp4bb] Saxs reviews or books

Hi Rojan, This paper may be more on the intermediate level, but is certainly worth a read. Koch MH, Vachette P, Svergun DI. Q Rev Biophys. Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. 2003 May; 36(2): 147-227. htt

Re: [ccp4bb] refinement problem

Dear D.L., I suspect the issue is in determining the correct space group. Sharing the Rmerge and current space group would be useful. Take Care, Sean http://store.p212121.com/

Re: [ccp4bb] Heavy atom salt at low pH

You may want to try the Heavy-atom Database System http://hatodas.harima.riken.go.jp/ Version 2 (http://hatodas.harima.riken.go.jp/hatodas_v2/query/queryheavy.jsp) allows for pH as a search option. http://hatodas.harima.riken.go.jp/hatodas_v2/query/queryheavy.jsp Hope that helps, Sean

Re: [ccp4bb] List of commonly used cryoprotectants and buffer molecules

>Dear All, > >I am trying to find out which molecules are frequently used by X-ray >crystallographers serving as cryoprotectants or as buffer molecules. The >idea behind this is to sort native ligands from molecules that appeared in >the electron density just because they were used in the crysta

Re: [ccp4bb] Problem with getting protein-inhibitor complex structure

>Dear all, >We are working on protein-inhibitor complex crystal structures, although > we did get nice crystals and soaked them with >inhibitor for several days, > all structures we obtained were empty!!There are nothing at the active site. > For several crystals. >their color turned very cl

Re: [ccp4bb] attachments

How about having people just link to uploaded photos on flickr (http://www.flickr.com/) or similar free service? If you upload the photos and select 'all images' a link is produced that can be easily shared (http://farm5.static.flickr.com/4134/4755503052_bc6835dcdc.jpg). CCP4 doesn't have wor

Re: [ccp4bb] Mysterious Crystals?

Perhaps this is a case of a 'phantom crystal' that was discussed on the CCP4bb awhile back: http://bit.ly/b6Rgw7 All the Best, Sean

Re: [ccp4bb] 2,3-butanediol

Dear all, I would like to know which is the more suitable method of using 2,3-Butanediol as cryoprotectant? Addition in to reservoir buffer or crystal soaking or both can be tried? Cheers Gauri -- I am sure both could be tried, but have found quite few papers mentioning brief soaking with 2

Re: [ccp4bb] Why Do Phases Dominate?

I found the paper "An Excel Spreadsheet for a One-Dimensional Fourier Map in X-Ray Crystallography" by William Clegg quite helpful. The paper includes a supplemental spreadsheet in which you can adjust various contributions of phase and amplitude. I wrote an outline of the first part of the pape

Re: [ccp4bb] program to display space group symmetry in three dimensions

On Tue, 16 Mar 2010 20:11:29 -0400, Karthik S wrote: >Hi, I was looking around for programs that display space group symmetry >information and could not find any but perhaps i am lost for valuable or >relevant keywords. >I found two references TABLES and CRYST, but are there other alternatives >t

Re: [ccp4bb] homology modelling using sequence alignment

>I am trying to create a homology model of a coiled-coil for use in molecular >replacement. I have a template poly-ala coiled coil that I like to use, so that is fine. >I want to thread my sequence onto the helix and am trying to find a server/easy >program that will do this. As a starting point

Re: [ccp4bb] cryoprotection for fragile crystals

I believe this is the article that you are looking for: http://www.xtals.org/crystal_cryo.pdf Cheers, Sean

Re: [ccp4bb] Alternatives to ChemDraw 3D

> You can build any 3D molecule easily in Discovery Studio Visualizer - It is free but > not for Mac OS I have been pretty impressed with Discovery Studio Visualizer and feel that it can serve as a nice compliment to Pymol. I wrote up a brief overview and comparison between the two programs her

Re: [ccp4bb] question on the effect of a fire alarm on crystallization

We are going to be a pretty unpopular bunch if this thread concludes that we need to set off fire alarms in order to nucleate our crystals. :) Sean

Re: [ccp4bb] [off topic] another network

I wanted to follow up on this 'older' thread and let people know that I have updated the RSS feed to now include 26 resources. The feed now generates about 1500 articles that are continuously updated, which is a bit much to read. Therefore, over the next day or so I'm going to offer to create a c

Re: [ccp4bb] Retraction of 12 Structures

On Thu, 10 Dec 2009 13:06:36 -0600, Tanner, John J. wrote: >Some of you might be curious about the "Ajees et al debacle" that Jacob mentioned in his message. Here are two links: > >Nature Brief Communication that questioned the validity of one of Murthy's structures: > >http://www.nature.com/na

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....

On Fri, 11 Dec 2009 15:30:53 -0500, Ibrahim Moustafa wrote: >You are absolutely right, more information describing to what extents these >structures were falsified will be valuable to the community. Actually, it >will be more useful if the investigators can publish their report as an >article in

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures

Thanks for bringing this article to our attention. I went ahead and created a table of the PDBs in question including links to the structures, journals and citations. My hope is that it will save others time trying to track down this information. http://bit.ly/5KqaRF Hope it helps. Sean

Re: [ccp4bb] Methylation of macromolecular complexes

>I have a small complex, one component is 13 kDa with structure available and the other is 7 kDa, which could not be able to grew crystals after lots of efforts. It grew crystals after methylation and diffracted to 2.3 A, however, I could not be able to solve the structure using the structure of th

Re: [ccp4bb] Help me!!

Hello Raju, Welcome to crystallography! I don't have much information about predicting structures, but have put together a list of resources about protein crystallization: http://tinyurl.com/ygmbpa3 Happy reading :) Sean

Re: [ccp4bb] [off topic] another network

Hello Fred, Thanks for sharing! I have also been looking for ways to keep up on literature. This weekend, I combined 17 structural journals into a single RSS feed using yahoo pipes. I did a short post about it here: http://tinyurl.com/yhp2xlm I would be curious if others have any tips or tric

Re: [ccp4bb] Moving copies to be close to one unit cell.

Hello FX, As already mentioned there a number of programs that can perform this task. If you end up deciding to go with Coot, I put together a play by play that should help. http://bit.ly/oHqDW Hope that helps. Sean

Re: [ccp4bb] leonard TVþ

>I like any attempt to set up a proper science channel, but I don't think >it will solve the problem of too few people choosing to do science. >Neither will any Internet thing. The internet or tv will not solve the problem entirely, but I can say for certain that not every scientist is going

Re: [ccp4bb] [off-topic] new initiative for science TV

Hello Fred, Thanks for bring this to attention and am sure that it will receive support from those on the CCP4bb. I am huge a fan and supporter of science! I also feel that virtually any effort to spread the word about science and research should be taken. However, I am confident that the best

Re: [ccp4bb] r-factor does not reduce

Hello Sylvia, Two issues I would consider: 1) recheck the space group 2) make sure that I had selected a good model for my MR search All the Best, Sean

Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

I say deposit it both ways, someone needs to start keeping those computational chemists on their toes.

Re: [ccp4bb] images

questions or comments you may have. I will follow up with results in about a month. http://www.p212121.com/2009/06/04/do-we-need-an-x-ray-diffraction-image-data-bank/ Thanks. Sean Seaver