[ccp4bb] Postdoctoral Position at UCSF - Structure of Receptor Tyrosine Kinases

Date: May 16, 2012 11:35:34 AM PDT To: mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: Postdoctoral Position at UCSF - Structure of Receptor Tyrosine Kinases UNIVERSITY OF CALIFORNIA SAN FRANCISCO (UCSF) POSTDOCTORAL POSITION, JURA LAB Crystallographic studies of receptor tyrosine kinases A postdoctoral

Re: [ccp4bb] dm: Error in opening input map file.

Hi Eleanor, If you have a large protein and want to apply different ncs operations to different domains, then you might need to give multiple masks and matrices. Yu On Wed, May 16, 2012 at 8:26 AM, Eleanor Dodson wrote: > It is a long time since I did this, but don't you need just one master >

[ccp4bb] Postdoctoral Position at UCSF - Structure of Receptor Tyrosine Kinases

UNIVERSITY OF CALIFORNIA SAN FRANCISCO (UCSF) POSTDOCTORAL POSITION, JURA LAB Crystallographic studies of receptor tyrosine kinases A postdoctoral position in Receptor Tyrosine Kinase Structural Biology is available immediately for highly motivated individuals with a strong interest in crystallo

Re: [ccp4bb] correlations of B-factors and resolution

Please not that average B value may be arbitrary depending on data processing program, reference image etc. Average B values could be arbitrary (you can add to all atom single B value and it will not change information content of the data, they are removable). I think either variance of B or -

Re: [ccp4bb] correlations of B-factors and resolution

Hi, Thanks for all the suggestions and comments! I have 1635 reflections(5.0%)for the test set. PDB_REDO gives lower R and Rfree. Shall I refine it further and re-deposit it? Thanks! > Hi Tim, > > With small test sets, R-free doesn't become meaningless you just have to > take into account that R

Re: [ccp4bb] Strange Density

How about chloride? I know, there are negative electrostatics, but I think such is seen sometimes for halides. Or, is it possible that there is a side chain flipped? Jacob On Tue, May 15, 2012 at 9:51 AM, RHYS GRINTER < r.grinte...@research.gla.ac.uk> wrote: > Dear Community, > > As I'm a relati

Re: [ccp4bb] correlations of B-factors and resolution

Hi Tim, With small test sets, R-free doesn't become meaningless you just have to take into account that R-free has an error margin which is higher than for cases with a large test set. Few people report this error margin, but with a small data set you can easily do K-fold cross validation. I.e

Re: [ccp4bb] correlations of B-factors and resolution

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Qiang, without much explanation, rather from experience, the average B-factor rises as resolution drops. It does make sense in a way because high B-factors indicate some degree of disorder and disorder is usually the cause for the resolution limi

[ccp4bb] correlations of B-factors and resolution

Dear all, I have a 2.4A structure(pdb code 3LAF)with an average protein b-factor of 48. I wonder whether it's acceptable. Is there a direct correlation of b-factor and resolution? The R and Rfree are 21.1% and 23.1%, respectively. This structure has a very high solvent content, 75%. Does it affect

Re: [ccp4bb] dm: Error in opening input map file.

It is a long time since I did this, but don't you need just one master mask - then that is converted using your rotation matrix to mask the related part of the structure ? Eleanor Dodson On 15 May 2012 15:56, Yu Feng wrote: > Dear De-Feng Li, > > Thank you for your reply. Actually, I already us

Re: [ccp4bb] How to refine CNS output file in refmac

Those error messages are warnings - not fatal errors - there must be something else reported in the log file to cause that. But as Garib says DNA "standard" names vary according to program and year - see if your atom names are those in the $CLIBD/monomers/g/GUA.cif That is where REFMAC will find

Re: [ccp4bb] Baverage calculation

Baverage gives you a plot of B value against residue number and chain ID - that would allow you to visually see which parts of each structure are best ordered. If you have run TLS refinement and NOT used TSLANL to add the anise and individual contributions to B then the plot will give you the devia

[ccp4bb] Beamline Scientist Position at EMBL Hamburg

Dear all, we are looking for a highly motivated scientist to join the crystallography team at PETRA III. The successful candidate will support the commissioning of the two MX beamlines, their transformation into user facilities and will join the team supporting scientists using these facilities

Re: [ccp4bb] how to ignore spot overlap in imosflm?

Hi Xinghua, Your completeness is very low and even with a perfect model the quality of your maps will suffer. Two things may help if you have not already done them: 1) Merge the Friedel pairs. If you have kept F+ and F- apart so far, you could get significantly more complete data by merging t