Re: [ccp4bb] Poor Statistics for 2.1 Angstrom X-ray Dataset

Since the Xtriage agrees with R-free, data have some issues might be particularly at the spot identification level!What is the fraction of indexed vs unindexed spots reported by XDS- if you run the following two lines?grep -c " 0 0 0" SPOT.XDS# gives non-indexed spotsgrep -vc " 0 0 0" SPOT.X

Re: [ccp4bb] Analysing water molecules at protein interfaces

Hi Tommi, From my experience , pymol script might be one of the best options if not the best. Since you might want to consider the relative/normalized b factor for “bridging water” & want to visualize the distances & assess whether all makes sense; pymol script works great for all of those. Unfo

Re: [ccp4bb] Plasmids for Fluorescent proteins

Hi Prerna, Addgene is the first & best place to look for such commonly desired plasmids or proteins! Best, Reza Sent from my iPhone > On Jul 13, 2024, at 11:53 PM, P G wrote: > >  > Hello everyone, > We are looking for some fluorescent proteins for undergraduate research (GFP, > BFP, DsRed d

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

Hi Devbrat,Have you tried indexing using XDS multi-lattice processing? It is a very useful indexing process for multi-lattice and/or 2nd lattice interference with the major one. Best,Rezaul Karim, Ph.D.Structural Biology ScientistNurix Therapeutics Inc.Sent from my iPhoneOn Nov 15, 2023, at 6

Re: [ccp4bb] High Temperature Factors with TLS

If  the correct atoms are in place, resetting the b factors of those atoms/residues to a constant e.g. 5.00 and refining in phenix with individual B-factors ON should take care of these.Best,RezaSent from my iPhoneOn Aug 2, 2023, at 7:42 AM, Thomas, Leonard M. wrote: Hello All, A general qu

Re: [ccp4bb] missing covalent bond between asparagine and N-

- do readyset)Refine that pdb in Phenix without hydrogen.Then check it in coot & pymol. Even coot shows dotted lines, pymol will show a solid bond😀!Hope it helps! Best,Reza ________ Md Rezaul Karim, Ph.D. Postdoctoral Research Fellow Department of Drug Discovery H. Lee Moffitt

Re: [ccp4bb] To solve the problem of an extremely asymmetric

one of these could affect separation efficiency and/or peak characteristics. Regards,Reza “The rule for web content is to keep it short. The rule for email content is to keep it ultra-short.” — Jakob Nielsen, ‘king of usability’ ________ Md Rezaul Karim, Ph.D. Postdocto

Re: [ccp4bb] Best protocols to advance a low resolution twin

son B data (~95).  Thanks,Reza Md Rezaul Karim PhD candidate PhD Program in Integrated Biomedical Sciences Dept. of Molecular Medicine, Morsani College of Medicine, USF,Tampa Schonbrunn lab, Moffitt Cancer Center, Tampa Email: rez...@health.usf.edu, md.ka...@moffitt.org Phone: (813) 745 4673 ext.

Re: [ccp4bb] Best protocols to advance a low resolution twin

he mystery. Thanks,Reza Md Rezaul Karim PhD candidate PhD Program in Integrated Biomedical Sciences Dept. of Molecular Medicine, Morsani College of Medicine, USF,Tampa Schonbrunn lab, Moffitt Cancer Center, Tampa Email: rez...@health.usf.edu, md.ka...@moffitt.org Phone: (813) 745 4673 ext. 5462

Re: [ccp4bb] Best protocols to advance a low resolution twin

protein band on SDS at right MW. Data from 20+ crystals from various condition & additive screens came out all the same.Resorted to changing the construct to make variable N/C-term for future. Thanks,Reza Md Rezaul Karim Postdoctoral Research FellowH. Lee Moffitt Cancer Center

Re: [ccp4bb] Vote for cryoEM

(e.g. don't believe in climate change or it's a hoax) but don't listen to scientists- then twitter could be blamed, but science fails. Thanks,Reza Md. Rezaul Karim (Reza) Ph.D. candidate, PhD Program in Integrated Biomedical SciencesDepartment of Molecular MedicineMorsani College o

Re: [ccp4bb] aimless outputs mean intensities for friedel pairs

some clue whether this is the case. Another alternative is xdsconv. Any advantage of using pointless and aimless instead of xdsconv for your purpose? Thanks,Reza Md. Rezaul Karim (Reza) Ph.D. candidate, PhD Program in Integrated Biomedical SciencesDepartment of Molecular MedicineMorsani

Re: [ccp4bb] ITC Stoichiometry

Hi Angshu,Very interesting experiment. Is the B is in hexameric form in solution by itself or it requires A for hexamer formation? Thanks,Reza Md Rezaul Karim PhD candidate PhD Program in Integrated Biomedical Sciences Dept. of Molecular Medicine, Morsani College of Medicine, USF,Tampa Schonbrunn

Re: [ccp4bb] protein expression in human cells

In our lab, we see Expi293F works very good. Thanks, Reza Md. Rezaul Karim Graduate student, PhD Program in Integrated Biomedical SciencesMorsani College of Medicine University of South Florida E-mail: reza...@yahoo.com, rez...@health.usf.eduPhone: +1-954-937-8487 On Friday, January 24

Re: [ccp4bb] higher older tNCS

Hello Jessica,You are working on MR, but tNCS option comes during refinement. In phaser, if you provide 3 copy or 3 components during MR setup, does not it work? Phenix online documentation should be the most updated. Thanks,Reza Sent from Yahoo Mail on Android On Tue, Jul 23, 2019 at 11:17

Re: [ccp4bb] determining the point group and the space group

On Thu, Apr 19, 2018 at 11:32 AM, Rezaul Karim wrote: I think Graeme's point is right. This is the work expert crystallographer. By the way, DIALS could be used for XFEL data, as the program page & recent publication indicates. NB: I have no experience in XFEL data. Than