Re: [ccp4bb] First stucture of FCFV

2014-04-03 Thread Bernhard Rupp
Several people were asking what this FCFV tentacles actually might be. I think it is some fungus/yeast growing out of nutritious drops. Does resemble fungus/mushroom mycelium. I have also some that look like huge bacteriophages with nice heads on them, probably yeast buds. There is also a yeast

[ccp4bb] PhD position in Structural Biology in Norway

2014-04-03 Thread Hans-Petter Hersleth
Dear all, A 4-year PhD position in Structural Biology starting August 2014 is available at University of Oslo, Department of Biosciences, Section for Biochemistry and Molecular Biology. The position is funded by the Research Council of Norway and the University of Oslo. The project is

Re: [ccp4bb] First stucture of FCFV

2014-04-03 Thread Artem Evdokimov
Common molds like aspergillus or penicillium. After a while you sometimes get sporangia, then you can tell with more certainty. .. A. On Apr 3, 2014 3:50 AM, Bernhard Rupp hofkristall...@gmail.com wrote: Several people were asking what this FCFV tentacles actually might be. I think it is some

Re: [ccp4bb] First stucture of FCFV

2014-04-03 Thread Chad Brautigam
I once encountered mold-dependent crystallization of a protein.  Wouldn't that have made for a lively Methods section? Luckily, we determined the structure from crystals derived from a different, non-moldy condition.  Whew. Chad From: Artem Evdokimov

Re: [ccp4bb] First stucture of FCFV

2014-04-03 Thread Reza Khayat
I think fungus dependent crystallization has occurred for some labs. A paper that pops into mind is from my graduate laboratory (not my work though): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2225192/ Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of

Re: [ccp4bb] loggraph not popping up after refmac5 ccp4-6.4

2014-04-03 Thread hari jayaram
Hi all .. loggraph seems to be broken on Redhat 6.5 . It may be a blt error. Can someone confirm that they can get loggraph to work on Redhat Enterprise 6.5 with the ccp4 provided binaries. Sadly Redhat nor Activestate provide blt replacements In all cases the loggraph starts a blank window

Re: [ccp4bb] First stucture of FCFV

2014-04-03 Thread Patrick Shaw Stewart
Those who use lysozyme as a model protein should note that fungal spores of an unknown strain can have a dramatic effect on lysozyme crystal nucleation, as noticed by my student many years ago (I wasn't completely happy with the report because we never knew what we were working with!). Chayen, N.

[ccp4bb] Problem with making covalent bonds in phenix by LINK or edits file

2014-04-03 Thread Xiaoming Ren
Dear all: I am encountering a problem. I built a monomer model which is a modified nucleotide with Sketcher in ccp4 suite and generated the .cif file of this monomer. However, I could not make it bind with other nucleotides in the nucleic acid chain. I have tried to write LINK lines into PDB

Re: [ccp4bb] Problem with making covalent bonds in phenix by LINK or edits file

2014-04-03 Thread Nigel Moriarty
Xiaoming Can you send me the three residues in question (or the whole model) and the files you have so I can point you in the right direction. Cheers Nigel On Thu, Apr 3, 2014 at 1:17 PM, Xiaoming Ren xiaomingre...@gmail.comwrote: Dear all: I am encountering a problem. I built a monomer

Re: [ccp4bb] Problem with making covalent bonds in phenix by LINK or edits file

2014-04-03 Thread Joel Tyndall
Dear Xiaoming, I would try using the graphical interface within phenix refine to add in the bond length/angle constraints for your link. This seemed to work fine with our system without actually needing a link record. J -Original Message- From: CCP4 bulletin board