[ccp4bb] Scripps LCP workshop

Hello all, I’d like point you all to the LCP Tool and Technologies Workshop that the Scripps Research Institute is hosting in Bedford, MA on October 17th. The workshop is being run by Dr. Vadim Cherezov, and is part of a two day protein crystallography event in Bedford, MA. Please see here for mor

Re: [ccp4bb] rigaku micromax 007 cooling

Hi Ours is cooled by a Haskris R250, which is sized for an XStream also. While our heat exchangers have had a couple of issues, overall the Haskris heat exchangers have performed quite well. They redesigned ours when they found out about our building chilled water. I'm not affiliated with and hear

Re: [ccp4bb] moleman2 install problem

Hmm. Maybe I'm doing something very wrong, because I get the following when I try those binaries: dyld: Library not loaded: /usr/local/gfortran/lib/libgfortran.3.dylib Referenced from: /Users/brooks/Downloads/usf_osx_bin/./moleman2 Reason: no suitable image found. Did find: /usr/local/gfor

Re: [ccp4bb] rigaku micromax 007 cooling

Hi Andreas - My 007HF is cooled by a Haskris R050 chiller which I got from Rigaku. This has a refrigeration loop inside it to extract heat from the closed water loop that goes to the generator; the extracted heat can then go to building chilled water, or even an open loop (city cold water, th

Re: [ccp4bb] rigaku micromax 007 cooling

Thermo scientific has air/water chillers. Google: thermo scientific neslab merlin recirculating chillers brings up the links. We have one of these cooling an Oxford xcalibur. It supplies circulating cold water under pressure which we hook up where the house chilled water would go on the water/waer

Re: [ccp4bb] rigaku micromax 007 cooling

Dear Andreas, We have a Hyfra water cooled system (VWK50) on our MicroMax 007, but it is probably over-dimensioned because it is also used by a Xstream equipment, a smaller dedicated cooler to the micromax could be better. Daniel Le 24/07/2014 17:53, Andreas Förster a écrit : Dear all,

Re: [ccp4bb] rigaku micromax 007 cooling

I would warn you that the K3 and K9 chillers have internal hoses which cannot tollerate water pressure above 125 psi.  We had a hose fail from the building chilled loop pressure.  So, be careful adding any pressure with a pump before the chiller...and maybe consider one after the chiller to pull

Re: [ccp4bb] rigaku micromax 007 cooling

Dear Andreas, we had a similar issue with our MicroMax 007, with a primary water/water chiller (ATC K3) in between the generator and a secondary inhouse water circuit. After a year of reliable service the K3 would shut off occasionally and dump the 007 with a cooling error. We found that th

[ccp4bb] rigaku micromax 007 cooling

Dear all, I have a Rigaku MicroMax 007 HF X-ray generator that is cooled by chilled water supplied rather unreliably through the building infrastructure. I was wondering what alternatives exist. Could other MicroMax 007 users share their experiences with alternative cooling solutions with m

Re: [ccp4bb] Problem in molecular replacement

You can use molrep or phaser as you prefer with DNA. To do that, you can edit you pdb file by hand with your favorit text editor (vim, emacs...) And you can cure your pdb file with Edit PDB File in ccp4 coordinate Utilities De : dusky dew [duskyde...@gmail.

Re: [ccp4bb] moleman2 install problem

Hi Tim, Thank you! yes, I download it through ftp from xray.bmc.uu.se I got it from pub/gerard/xutil_osx I couldn’t find usf_osx_bin/moleman2 Does anyone know how to find it ? Thanks! Yamei Yu State Key Laboratory of Biotherapy／Collaborative

Re: [ccp4bb] Problem in molecular replacement

How do I use DNA as search model? Can I use it in molrep or phaser? On Thursday, July 24, 2014, FOOS Nicolas wrote: > Dear Yang, > > you should try different search model, for example : > 1) DNA only, > > 1) DNA > 2) protein > > 1)DNA+Prot > > etc... You can also try to find a partial solution an

Re: [ccp4bb] moleman2 install problem

Hi Mark Unless you've done something very odd, Snow Leopard binaries should be compatible with Mavericks (and Yosemite, too, when you get to try that). Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus,

Re: [ccp4bb] moleman2 install problem

Hi Yamei, If you're on OS X version 10.9.3, then I guess you're on Mavericks, not Snow Leopard ( https://www.apple.com/uk/osx/ ). Therefore, I guess you will need to download the source code and recompile it, since I don't know that Snow Leopard binaries are compatible with Maveric

Re: [ccp4bb] Problem in molecular replacement

Dear Yang, you should try different search model, for example : 1) DNA only, 1) DNA 2) protein 1)DNA+Prot etc... You can also try to find a partial solution and keep this solution to place the other molecules with another round of MR. Be careful if you use only DNA, if the density doesn't sho

Re: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation?

Not sure why this qualifies as a flame or who you want to flame - seems reasonable but needs to be done so that the data items are extracted consistently from all programs and can be interpreted again by the refinement (or validation) programs independently of which program they came from. Insular

Re: [ccp4bb] moleman2 install problem

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Yamei, I am not sure where the official site for USF is now, but I would use http://xray.bmc.uu.se/usf/ There you can download OSX_binaries for Lion and Snow Leopard. The file in the tar-archive is called 'usf_osx_bin/moleman2' rather than osx_m

Re: [ccp4bb] Problem in molecular replacement

In addition to that good suggestion, with a model at such high sequence identity and with reasonable resolution data, it would be a good idea to search for smaller models, like a single dimer or even a monomer, because the assembly may have changed conformation. Another possibility you should c

Re: [ccp4bb] moleman2 install problem

Hi Tim, I download it again through command line and got another error message:” -bash: /Users/yamei/xutil_osx/osx_moleman2: Bad CPU type in executable It seems the software does match my CPU. The processor of my computer is: 2.3 GHz Intel Core i7 Do you know how to solve this ? Thank you so muc

Re: [ccp4bb] Problem in molecular replacement

Try using DNA as a search model - this has worked very successfully in our hands before. Tony. - - - - - - - - - - - - - - - - - - Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton,

[ccp4bb] Problem in molecular replacement

DEAR ALL I am trying to solve the structure of a protein DNA complex with molecular replacement. The resolution in about 2.5 angstrom. The spacegroup is P21. The search model has about 50% identity and is a dimer of a dimer. The problem is the unit cell is huge and so the number of molecules in as

Re: [ccp4bb] hi - history of protein crystallization

Hi Sanjit, These two reviews throw some light on the history of protein crystallization: http://www.ncbi.nlm.nih.gov/pubmed/24165393 http://www.ncbi.nlm.nih.gov/pubmed/25005076 I didn't understand what you exactly mean by " properties of protein crystal in lattice parameters" .

[ccp4bb] 2014: Crystal (cl)Year gentle reminder

Dear all, the early bird registration deadline (July 30th) is approaching fast! Register the soonest to have a discounted fare. Students and young researchers: there are some slots available for oral presentations and some funds left for travel grants. Submit your abstracts http://www.n

Re: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 [flame] It's all there in the shelx format. If someone would write a wrapper to translate it into mmCIF, everybody would be happy with the least necessary effort [/flame] ;-) Cheers, Tim On 07/24/2014 10:46 AM, Bernhard Rupp wrote: > From a practical

Re: [ccp4bb] moleman2 install problem

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear yamei, my guess is that the download was not completed, or your hard disk is about to break. Try downloading it again. You can also copy files from the command line with the cp command. Best, Tim On 07/24/2014 07:19 AM, Yamei Yu wrote: > Hi all

[ccp4bb] hi

Hello to every one Can any body send me the information in concise form about history of protein crystallization along with some idea about the properties of protein crystal in lattice parameters. Thanks In advance Sanjit Kumar

Re: [ccp4bb] Protein Crystallography challenges Standard Model precision

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi James, I would say that 0.333 (in a scientific context) implies that I am confident about this number up to the third decimal point, i.e. 0.3325 <= x <= 0.3334. This gives you an idea of the precision. 1/3 is not a scientific format, but a mathemat

[ccp4bb] hi

Hello to every one Can any body send me the information in concise form about history of protein crystallization along with what is the properties of protein crystal in lattice parameters. Thanks In advance Sanjit Kumar

Re: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation?

>From a practical point of view, a solution for documenting grouped occupancy refinement should at minimum allow (a) easy & automatic harvesting from the respective refinement log files, and (b) equally easy extraction from the PDB/cif format to replicate the same refinement (c)not m