Re: [ccp4bb] replacing B-factor column and color accordingly

Hi Yahui, using a text editor like Mac TextEdit you can also click the option key (cursor will change to cross shape), click and drag to select column, copy and paste. All the best,John On Monday, January 13, 2025 at 09:02:49 AM CST, Hui YAN wrote: Happy New Year, everyone! I am look

Re: [ccp4bb] 图片1

Hi there, all good suggestions to optimize crystals, here are few other things to try: 1. Spin down your protein sample in a centrifuge prior to setting up trays to remove protein aggregates.2. Incubate trays at lower temperatures (for example if crystals grow at RT, try 15 and 4 C).3. Try stre

Re: [ccp4bb] Problem of data reprocessing with XDS

s > more accurate results, but may use more computing time. > > Hope this helps, > Kay > > On Sat, 5 Oct 2024 13:45:59 +, John Bacik wrote: > > > Dear Kay, do have any more information or would you mind explaining a > bit more what changes in the XDS code led to

Re: [ccp4bb] Problem of data reprocessing with XDS

Dear Kay, do have any more information or would you mind explaining a bit more what changes in the XDS code led to these significantly different statistics in the different XDS versions? Thanks,John On Wednesday, October 2, 2024 at 02:35:25 PM CDT, Kay Diederichs wrote: Dear Yimin,

Re: [ccp4bb] Presence of negative density in Sim Omit map

lletin board on behalf of John Bacik <b45abf420e1f-dmarc-requ...@jiscmail.ac.uk> Sent: Friday, July 26, 2024 11:18 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Presence of negative density in Sim Omit map  | | You don't often get email from b45abf420e1f-dmarc-requ...@jis

Re: [ccp4bb] Presence of negative density in Sim Omit map

Green StreetUniversity of GeorgiaAthens, GA 30602Tel: (706) 583 0303From: CCP4 bulletin board on behalf of John Bacik <b45abf420e1f-dmarc-requ...@jiscmail.ac.uk> Sent: Thursday, July 25, 2024 12:21 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Presence of negative density in

Re: [ccp4bb] Presence of negative density in Sim Omit map

o localized around the peak - depending on your low-res cutoff. As John Bacik suggested you should check for a mis-modeled part of a symm-related molecule, but if that were the case, you should see the red density even before omitting the loop, and you should see the red density somewhere

Re: [ccp4bb] Presence of negative density in Sim Omit map

Hi Renu, you may try using a Polder omit map for the region rather than a simulated annealing map. You may also check if the red density is due to a symmetry related molecule that is not modeled well. Hope it helps. JP On Tuesday, July 23, 2024 at 04:50:00 PM CDT, Renuka Kadirvelraj

Re: [ccp4bb] solvent mask for partial ligands, addendum

Hi Gottfried, I was wondering what happens if you make a Polder omit map for the HEPES? I am also curious, if the extra positive density is for missing bulk solvent with ligand of occupany 0.5, do you observe the density with ligand present at 0.5 occupancy to be more diffuse than with no liga

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

Hi Devbrat, here are a couple of other things to try: - When screening crystals use rastering to find regions of the sample where multiple lattices may be less problematic. If multiple lattices are observed, often regions on the crystal(s) close to the edge will not be as affected by twinning/

[ccp4bb] DEADLINE EXTENDED: CALL FOR PROPOSALS: neutron beam time at the Protein Crystallography Station at LANL

http://lansce.lanl.gov/lujan/instruments/PCS.shtml. We strongly encourage you to contact us for questions concerning sample preparation, instrument capabilities, sample environments, and/or proposal preparation. Julian Chen, che...@lanl.gov John Bacik, jba...@lanl.gov Clifford Unkefer, c

Re: [ccp4bb] crystal

Hi Shivesh, Have you tried dropping your MPD concentration (ie. by increments of ~5%)? Changing the pH may also result in larger crystals. JP On 1/30/07, shivesh kumar <[EMAIL PROTECTED]> wrote: Dear all Sorry for unrelated query.I have crystallized a protein which is at 40% of MPD.But the p