Re: [ccp4bb] Phasing with Many Monomers/AU

I am grateful for all of the suggestions. I think I have enough tricks to try at this point, but I may check back with this group if things don't work out. Many thanks once again, Chris On Sat, Jan 18, 2014 at 11:14 AM, Chris Fage wrote: > Hello Everyone, > > I am currently trying to phase a s

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Re: [ccp4bb] How to show the ligands (both as sticks and sphere) as shown here in Pymol

Not a pymol approach but I've noticed this dual mode display with transparency is the default in Molsoft ICM browser if you toggle on  ball and sticks together with spacefill for the same atoms. Molsoft ball-and-stick also shows the bond order or aromaticity of ligand atoms - which I guess is a

Re: [ccp4bb] How to show the ligands (both as sticks and sphere) as shown here in Pymol

Hi guys, Thank you so much for the suggestions! The suggestion to "make two objects of your ligand, display one as sphere and the other as stick. Then change the transparency setting for the spheres" works!! This way, the sphere and the stick can colored differently. And, I also found that show the

Re: [ccp4bb] Phasing with Many Monomers/AU

Hi, In the past I had two cases where seemingly unsuccessful MR became successful simply by collecting the missing cusp, which is due to exist in your P1 case if you collected your data by rotation of the crystal around a single orientation. However, I don't know if modern MR programs use techn

Re: [ccp4bb] Phasing with Many Monomers/AU

It will be useful if you share the unit cell dimensions, may be it belongs to a higher symmetry, given the low resolution, you may have missed it out. Sridhar From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eugene Valkov Sent: Monday, January 20, 2014 6:37 AM To: CCP4

Re: [ccp4bb] Phasing with Many Monomers/AU

What is the sequence identity of your best search model? Finding that many copies in P1 with 3A data is a challenge but certainly not impossible if there is a reasonably close (>20-25% identity) search model available. I would suggest spending some time on preparing a very good search model with to

Re: [ccp4bb] Phasing with Many Monomers/AU

I agree. Searching with a larger unit is likely to be successful if you have a good idea of the structure of that larger unit. We had an example of a low homology (29% identity) MR situation with 8 subunits per ASU with twinned data. Not solvable with monomers. Solvable with a dimer search mode

Re: [ccp4bb] Phasing with Many Monomers/AU

Is the monomer the biggest unit you have to search with? If there is a dimer, tetramer, etc. that is conserved, you could try searching with that. On 01/19/14 14:30, Chris Fage wrote: Thank you all for your responses. I already have a few ideas about how to approach the problem. One of my c

Re: [ccp4bb] How to show the ligands (both as sticks and sphere) as shown here in Pymol

Hi Wei, I think it's easier to do with a surface representation. I'd do something like this: # start script fetch 3b6a, async=0 as cartoon extract ligand, c. c and organic util.chainbow("3b6a") color green, elem c and ligand color oxygen, elem o and ligand show surface, ligand set surfac

Re: [ccp4bb] How to show the ligands (both as sticks and sphere) as shown here in Pymol

Hi Wei *Dead easy* in ccp4mg - display your object as ball and stick, clone it, then display the clone with reduced opacity (or increased transparency). On 20 Jan 2014, at 04:40, Wei Shi wrote: > Hi all, > Please see attached Fig where they show the ligand both as sticks and spheres > at the