Re: [ccp4bb] Beamline Stability Issues

2008-07-28 Thread Julian Adams
Dear Lucas It looks to me that the angle of the VCM and therefore of the reflected pink beam which has double the angular change may be your major contributor. This could be coupled and complicated by any vertical movement in the source. Things I would look at are the motors on the kinematic j

Re: [ccp4bb] estimate protein in Incl bod

2008-07-28 Thread Chun Luo
You can solibilize IB with your solublization buffer, measure the solubilized protein concentration by a protein assay like Bradford. Then adjust the concentration. Most weight of IBs is not from proteins. However, your protein should be the predominant protein in the IB if the expression is done

[ccp4bb] estimate protein in Incl bod

2008-07-28 Thread Meg
We have our recombinant protein expressed in inclusion bodies we just wash the IBs and perform solubilization and refolding. Our solubilisation protocol mentions making up the volume to contain 7-8 mg / ml protein. 1. how can we determine the total protein content in the inclusion bodies itself

Re: [ccp4bb] off-topic: protein crystallography in organic chemistry lab

2008-07-28 Thread Artem Evdokimov
Hi, I assume that there is no other way and you have to share the space, so I will save you from the standard tirade about functional space segregation :-) If the air in the lab is so loaded with solvents that your plates are melting - then *you* (or anyone else for that matter) certainly s

Re: [ccp4bb] question about getting rid of model bias in refinement

2008-07-28 Thread Anastassis Perrakis
If resolution is around 2.0 or better, ARP/wARP is particularly powerful for such cases when model bias needs to be reduced. For more info: http://www.ncbi.nlm.nih.gov/pubmed/18094467?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum http://www.ncbi.nlm.nih.g

[ccp4bb] off-topic: protein crystallography in organic chemistry lab

2008-07-28 Thread Uma Katre
Dear all, Sorry for an extremely off-topic question, but I thought this would be the best place to find an answer. We are setting up our protein crystallography lab and have been asked to share laboratory space with an organic chemistry group which is already well established in the room. Th

Re: [ccp4bb] Refinement problem

2008-07-28 Thread Clemens Vonrhein
Hi Sampath, On Sat, Jul 26, 2008 at 02:05:17AM +0900, Sampath Natarajan wrote: > Also I could find many cuts in the density. This looks to me like a problem with your low-resolution data? Since you collected 1.6A data my guess is that you probably had a fair amount of overloads. Did you do a low-

[ccp4bb] Beamline Stability Issues

2008-07-28 Thread Lucas Sanfelici
Hello Michele! Thanks for your answer!... Answering your questions we have a collimating mirror upstream the mono and the water temperature used to keep this guy cooled is within +/-0.3°C. Regarding fluctuation in the water flow, I don’t know, maybe not ‘cause we have a dedicated thermal bath wit

[ccp4bb] sfcheck output file and rscc

2008-07-28 Thread Ariel Talavera
Hi there, Following the instructions I got from the mail list (thanks to them) I ran sfchek to get the rscc. When I did it I could nor find the exact term of rscc but there is a "Correlation Factor" into the Model vs. Structure Factor chart. Is that "Correlation Factor" the rscc I am looking

[ccp4bb] Thanks

2008-07-28 Thread Sampath Natarajan
Dear all, Thank you so much for the good responses. I will try to get good model again with your suggessions. If I have problem again I will let you know. Thank you very much again for your suggessions who are all responded me. With Regards, Sampath

[ccp4bb] carrection, rscc

2008-07-28 Thread Ariel Talavera
Hi again, I am trying to calculate the rscc of the model to the electron density map. Any help will be appreciated. Thanks, Ariel -- Ariel Talavera, Lic. Dept. of Computational and Structural Biology Center of Molecular Immunology P.O.Box 16040, Havana 11600 Cuba tel: (53-7) 271 7933, ext. 21

[ccp4bb] rcss, how to

2008-07-28 Thread Ariel Talavera
Hi every one, Please, I need help to calculate the rcss. Thnaks in advanced, Ariel -- Ariel Talavera, Lic. Dept. of Computational and Structural Biology Center of Molecular Immunology P.O.Box 16040, Havana 11600 Cuba tel: (53-7) 271 7933, ext. 219 fax: (53-7) 272 0644 email: [EMAIL PROTECTED]

Re: [ccp4bb] CCP4MG can't start

2008-07-28 Thread Kendall Nettles
Hi Bill, I commented out the export DISPLAY lines, but it didn't help. What did fix it was reinstalling x11 from the OSX 10.5 CD. Any ideas? I've attached the launch script as a text file. Thanks! Kendall On 7/25/08 12:27 PM, "William G. Scott" <[EMAIL PROTECTED]> wrote: > Hi Kendall: > > I h