Re: [ccp4bb] calculating solvent volume from molecular surfaces

Alastair Fyfe wrote: Does anyone know of software that will segment a unit cell into volume internal/external to a calculated molecular surface ? thanks! Alastair Fyfe Well, if the surface was generated from some sort of model it is easy to mask the unit cell map to set all the volume intern

[ccp4bb] calculating solvent volume from molecular surfaces

Does anyone know of software that will segment a unit cell into volume internal/external to a calculated molecular surface ? thanks! Alastair Fyfe

Re: [ccp4bb] monomer-dimer

I agree completely with Anastassis that the equilibrium will be effected by changing the concentration of the sample during gel filtration, however I wanted to point out that the elution volumes of the two species are independent of their populations. I apologize if I was misleading. Mike ---

Re: [ccp4bb] monomer-dimer

Hi Maia, this review and website might be a good place to start: http://analyticalultracentrifugation.com/images/AUCinProteinScience.pdf http://analyticalultracentrifugation.com/default.htm Kushol Kushol Gupta, Ph.D. Research Associate Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School o

[ccp4bb] advice for processing data from multiple small wedges

I am having problems processing data from multiple wedges of 5-20 degrees each. I am working with data from microcrystals collected at a minibeam. I want to use the data for molecular replacement. I can usually only collect about 10-15 frames before the crystal is obviously radiation damaged.

Re: [ccp4bb] monomer-dimer

Hi ccp4bb Could you please send me some references with the sedimentation equilibrium calculations of Kd, monomer/dimer ratio etc. Maia Maia Cherney wrote: Thank you. Now I understand the difference. I thought there was separation. Maia Xuewu Zhang wrote: Hi Maia, I have seen your post r

Re: [ccp4bb] monomer-dimer

Thank you. Now I understand the difference. I thought there was separation. Maia Xuewu Zhang wrote: Hi Maia, I have seen your post regarding this before and I just want to point out that you may have confused "AUC" (analytical ultracentrifugation) with gradient-based ultra-centrifugation meth

Re: [ccp4bb] process data in R32

If you cant import a file with symmetry labelled R32 but with a=b and alpha=beta = 90, and gamma = 120 then something is wrong - the symmetry checking looks at both name and cell.. or at least it used to.. The output mtz would have symmetry name changed to H32, but that is just a name - in ea

[ccp4bb] process data in R32

Hi, I have read all of the past messages about the confusion of H32 and R32 and I want to get the correct indexing sp that I can import the .sca file into CCP4.. I use DENZO and SCALEPACK in HKL2000. If you read the manual then it states that space group R32 should only be autoindexed by DENZO

Re: [ccp4bb] To view the 2mFo-DFc map generated by SIGMAA

Hi Eleanor, I hate to disagree with you, even partially, but it depends on whether or not you're doing phase combination with external phases. In the usual case with just model information, SIGMAA doesn't take the absolute value of 2mFo-DFc so it can be positive or negative and goes with the o

[ccp4bb] About using COOT

Dear all, My protein has two chains A & B. The space gp is P212121. If I want to have a new PDB file containing the symmetry-equivalent molecule of B (x+1/2, -y+1/2, z+(0 -1 0)), and keep the chain A (x,y,z) unchanged. How can I do this COOT? many thanks for this help. stephen -- Dr. Stephen

Re: [ccp4bb] To view the 2mFo-DFc map generated by SIGMAA

Actually I think it needs the labels FWT PHWT I may be wrong but like REFMAC I think it outputs a ositive FWT and PHWT is either equal to PHIC or to PHHIC+180, depending on the sign og FWT = (2m|Fo| - D|Fc|) Eleanor Hailiang Zhang wrote: Dear Tim: This is also what I thought. Thanks! B

[ccp4bb] Call for MX-beamtime at HZB-BESSY II, Berlin, period: January/2011 - December/2011, Deadline: September 1. 2010

Next MX-proposal application deadline: September 1, 2010 See: http://www.bessy.de/boat/ We kindly request new MX-proposals for beamtime applications for the next beamtime period. In order to apply for beamtime, please register at the HZB on-line access tool "BOAT" (http://www.b

Re: [ccp4bb] monomer-dimer

Dear all, If I may add that I find the statement "First, remember that gel filtration elution volumes are independent of conditions like flow rate and protein concentration (unless there are nonspecific interactions at high concentration), but like I described before temp is a factor."

[ccp4bb] Jobs at NKI, in the group of Peter Peters.

*** these jobs are not for my group, I am posting this on request from my colleague Prof. Peter Peters, an electron microscopist. Do not reply to me. If you reply to me I promise I will not forward your email to Peter ... consider it as form of pre-selection of candidates ... *** Peter Pe