Re: [ccp4bb] Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB

community can come up with an answer, then I am sure we can convince PDB to add those information. Best, Rams. S. Ramaswamy Department of Biochemistry University of Iowa. On Wed, 2008-03-12 at 14:20 -0700, Dale Tronrud wrote: > Hi, > > I am looking over a number of models from the PDB

[ccp4bb] Off-topic structural genomics related question.

appreciate if they are shared with me (along with the assumptions that have gone into the calculations). Thanks. Rams. S. Ramaswamy. Department of Biochemistry University of Iowa.

[ccp4bb] Buried lysines!

Hello all, Is there any recent paper that contains an analysis of buried lysines in the PDB? Thanks. Rams. -- Ramaswamy. S Department of Biochemistry Roy J and Lucille A Carver College of Medicine The University of Iowa.

Re: [ccp4bb] Low resol structure

Dear Jim, The funny part is that the same journals will publish NMR structures. In terms of data/parameter ratio or in terms of comparing quality (Battacharya, Tejero and Montelione, Proteins:structure function genetics 66:778-795), the good NMR structures are about 2.5A resolution and most NMR

[ccp4bb] PARST 95 !

Dear All, I have a protein structure refined using full matrix refinement -SHELXL. When I was a small molecule guy, I used to use a program called PARST from Prof. Nardelli to analyze the coordinates. I googled to see if I can find a place to access the program - with no success. Does any one k

[ccp4bb] Found PARST!

Thanks All, I found it at http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/nardelli/pub/nardelli/ Rams.

Re: [ccp4bb] CCP4i under M1Pro

Hi Kelvin, I have the same problem. Cheers! Rams subra...@purdue.edu On Jun 28, 2022, at 11:45 AM, Lau Kelvin <5aaf8435dbef-dmarc-requ...@jiscmail.ac.uk> wrote: External Email: Use caution with atta

[ccp4bb] Map superposition!

Hi All, I have two maps - both cryo-EM. One with and one without ligand. I am trying to superpose them and I cannot seem to get ChimeraX to work. I then tried VESPER and that also does not work. The built models superpose very well. What is the best way to superpose maps. Thank you. Rams

Re: [ccp4bb] Map superposition!

boxes (unit cells) and symmetry can be different, gridding can be different too. I can help off list should you need any assistance! Pavel On Wed, Jan 25, 2023 at 6:30 AM Subramanian, Ramaswamy mailto:subra...@purdue.edu>> wrote: Hi All, I have two maps - both cryo-EM. One with a

Re: [ccp4bb] Lys-Arg crosslink?

Is there enough density for Glucosepane? Rams subra...@purdue.edu On Feb 25, 2023, at 1:42 PM, Celia Goulding wrote: External Email: Use caution with attachments, links, or sharing data In a recent structure we found strong electron density between a closely positioned Arginine

Re: [ccp4bb] To Trim or Not to To Trim

Dear All, I am kind of in agreement with Manfred, but I also have concerns. The RCSB and the databases are public databases used by non-structural biology experts a lot. They take the model as if it is an experimental result - rather than it being a model. Example: I just got a paper with re

[ccp4bb] Structure prediction - waiting to happen

Dear All, I am unsure if all other groups will get it - but I am sure this group will understand the frustration. My NIH grant did not get funded. A few genuine comments - they make excellent sense. We will fix that. One major comment is, “Structures can be predicted by alpfafold and other

Re: [ccp4bb] Structure prediction - waiting to happen

Ian, Thank you. This is not an April fools.. Rams subra...@purdue.edu On Apr 1, 2023, at 10:46 AM, Ian Tickle wrote: External Email: Use caution with attachments, links, or sharing data Hi Ramaswamy I assume this is an April Fool's but it's still a serious question be

[ccp4bb] Ligand superposition!

Hi All, I have over 50 pdb files that I have downloaded from PDB that all have the same ligand bound. I wamt to superpose the ligands (and move the protein coordinates using that matrix). The goal is for me to see how difference in ligand environments in different complexes. Is there an easy

Re: [ccp4bb] Ligand superposition!

> Beer-Sheva 84105 > Israel > > E-mail: bshaa...@bgu.ac.il <mailto:bshaa...@bgu.ac.il> > Phone: 972-8-647-2220 > Fax: 972-8-647-2992 or 972-8-646-1710

[ccp4bb] Nobel prize for Alpha fold and protein design!

Dear All, I am sure many of you saw the announcement of the Nobel Prizes. I am glad for the recipients. This would not have been possible but for PDB and the other structural databases (they should have been one of the recipients) and all those who contributed structures to these databases;

Re: [ccp4bb] Words to avoid

These discussions remind me of a talk I heard from Shekar Mande, I think, about the role of crystallographers in the wars around the world, particularly how this community has stood up for fairness. I have never felt prouder to be part of this community. I believe that as scientists, we also ha