Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

x2. (I think it's fair to say that we couldn't have identified some density issues just using XP.) (A 2nd edition of the book would also be a great idea.) Best regards, Navdeep --- Navdeep Sidhu Germany Web: https://scholar.google.de/citations?user=ZqU1AE0J=de --- --- On 12.03.24

Re: [ccp4bb] Combating disinformation in science and other areas

t;You Can't Be Neutral On A Moving Train." There's also a nice book of his of the same name, with some alternative views on other issues you touch on.) Best regards, Navdeep --- Navdeep Sidhu Germany Web: https://scholar.google.de/citations?user=ZqU1AE0J=de --- On 15.02.24 04:40

Re: [ccp4bb] Suggestions to improve resolution of protein crystals

Dear Saurabh, It's well known that good-looking crystals can have poor internal order, and therefore yield poor diffraction, and vice versa. As others have pointed out, it's crucial to check the quality of diffraction at room temperature (RT). Just to add a bit to that: There's a nice book that

Re: [ccp4bb] Can twinning be seen in the diffraction pattern?

PS: For a microscopically visible example in proteins, see the lovely cubic insulin interpenetrating non-merohedral twin crystallized by Madhumati Sevvana (Fig. 11a; thankfully open-access article): Madhumati Sevvana, Michael Ruf, Isabel Uson, George M. Sheldrick and Regine Herbst-Irmer.

Re: [ccp4bb] Can twinning be seen in the diffraction pattern?

Far as I understand, twins may or may not have macroscopically recognizable features. Macroscopic (and microscopic) features like face angles, reaction on etching, polarization of light, etc. can sometimes indicate twinning for at least a subset of cases, e.g. in diamond, some forms of quartz,

Re: [ccp4bb] AW: [ccp4bb] Can twinning be seen in the diffraction pattern?

Dear Marina, Just to add a couple of points, if you're using a Bruker machine, the programs RLATT can help visualize problem reflections; CELL_NOW is another program that can help. I found XDS to be useful in integration in such cases. You might also like to check out Regine Herbst-Irmer's

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

Hi Jacob, I don't quite see the scientific necessity. There already are good vaccines. If these are fine for the US and Europe, why aren't they fine for the rest of the world? Besides, the approach you suggest is fraught with risks. There is a non-coronavirus precedent for this. The oral polio

Re: [ccp4bb] Open position - data management in biophysics

Dear Gerlind, Markus, All: Well, sometimes the (written) promise of a 2-year contract also ends up boiling down systematically (for some PIs) to only a 6-month contract after all.--And that after you've spent half a year or more and multiple trips to the country concerned trying to get a work

Re: [ccp4bb] ligand bound to only one chain in the crystal

Dear Christian, Kleywegt (1996; "Use of Non-crystallographic Symmetry in Protein Structure Refinement." Acta Cryst D52, 842-857. DOI: 10.1107/S0907444995016477) reported that NCS-related molecules tend to be similar but differences in ligand binding do sometimes occur (cited Sevcik et al. 1996 in

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

mponents.pdf > > Cheers > > -- Ian > > > On Thu, 2 Jul 2020 at 11:58, Navdeep Sidhu <mailto:sid...@gmail.com>> wrote: > > Dear Ian, > > You seem to be slightly off there: The successful use of repeating > observations to reduce (especially sys

Re: [ccp4bb] Question about small molecule crystallography

Correction: It should read "with the detector almost but not quite hitting the source." On 02.07.20 17:13, Navdeep Sidhu wrote: > Alexander Blake wrote a nice chapter on small-molecule crystallization > in this book, if you run into problems in the crystallization stage: >

Re: [ccp4bb] Question about small molecule crystallography

Alexander Blake wrote a nice chapter on small-molecule crystallization in this book, if you run into problems in the crystallization stage: Alexander Blake. Crystal growth and evaluation (Chapter 3). In Clegg, William (Ed.) Crystal Structure Analysis: Principles and Practice. 2nd Edition.

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

Dear Ian, You seem to be slightly off there: The successful use of repeating observations to reduce (especially systematic) observational error predates von Neumann by at least 4 centuries. One of the first instances of its use was in the 1500s, due to a migrant scientist working in Denmark and

Re: [ccp4bb] Question about small molecule crystallography

Dear Jiyuan, There was a similar question on the bulletin board some 6 years ago; my response then (links below) complements some of the other great suggestions already made in answer to your question: , and

Re: [ccp4bb] Twinning in space group Pc

/twin laws in Pc please? Or any other suggestions are most welcome? Thank you very much Kristof --- Navdeep Sidhu Dept. of Neuropediatrics University of Goettingen Germany Email: nsi...@shelx.uni-ac.gwdg.de Homepage: http://shelx.uni-ac.gwdg.de/~nsidhu ---

Re: [ccp4bb] Rotamer Selection in Low Resolution Data

to place “optimal-fit to electron density side-chain rotamers into my model? Preferably in an NCS-independant manner? With thanks, Antony. --- Navdeep Sidhu University of Goettingen Germany Homepage: http://shelx.uni-ac.gwdg.de/~nsidhu ---

Re: [ccp4bb] Rotamer Selection in Low Resolution Data

PS: Just to clarify, my conclusion as to the usefulness of the program is based on results obtained in a shared research project. I did not directly use the program myself. Cheers, Navdeep On Thu, Jun 19, 2014 at 10:47:17PM +0200, Navdeep Sidhu wrote: Dear Antony, In addition to other good

Re: [ccp4bb] shelxc/hkl2map

to define the input file also along with shelxc. But instead of that i want to use GUI for that. How can i do that. Additionally i have installed hkl2map also and while i run it it asks for shelxc executable so how can i sort it out. Many thanx in advance Monica --- Navdeep Sidhu Departments

Re: [ccp4bb] sorry, sort of off topic

crystallisation and screening ahead of data collection! cheers Dean --- Navdeep Sidhu University of Goettingen ---

Re: [ccp4bb] small molecule crystallography

you'd agree with that assessment soon, after your first small molecule structure! Best, Navdeep --- Navdeep Sidhu University of Goettingen http://shelx.uni-ac.gwdg.de/~nsidhu/ --- --- On Tue, Mar 25, 2014 at 11:20:40PM +, Andreas Förster wrote: Thanks again for all the responses to my

Re: [ccp4bb] small molecule crystallography

software X to analyze data in space group P-43N would be welcome. Thanks. Andreas --- Navdeep Sidhu Departments of Structural Chemistry Pediatrics II University of Goettingen Office Address: Institute of Inorganic Chemistry Tammannstrasse 4 37077 Goettingen Germany Email: nsi...@shelx.uni

Re: [ccp4bb] large domain motion and calculation of flip flop angle

Dear Rajan, You could also use the CCP4 program LSQKAB (Kabsch, 1976): First superimpose domains 1 of the two conformational states. Then take this first overlay as the starting position and superimpose domains 2. The log file of LSQKAB should give the angle in going from the first to the

Re: [ccp4bb] Validity of Ion Sites in PDB

Dear Jacob, Another publication I found useful on this topic: Is the bond-valence method able to identify metal atoms in protein structures? Mueller et al. (2003). Acta Crystallogr. D59, 32-7. https://www.ncbi.nlm.nih.gov/pubmed/12499536 Best regards, Navdeep --- On Thu, Mar 06, 2014 at

Re: [ccp4bb] CELL_NOW Download

Dear Chen, To download CELL_NOW, please contact Bruker, http://www.bruker.com/. For a relevant tutorial for use in twinning, see e.g. Regine Herbst-Irmer's Introduction to Twinning at http://shelx.uni-ac.gwdg.de/~rherbst/twin/twin_introduction.pdf. In conjunction with CELL_NOW, I've also

Re: [ccp4bb] A question on crystal optimization

face and sharp edge crystal for my situation)? There is source says if the crystal grows too faster, the sharpness would be lost. Will you please also let me know how to slow down the growth rate of the crystal? Cheers, Acoot --- Navdeep Sidhu Departments of Structural Chemistry

Re: [ccp4bb] A question on the diffrentiattion of the salt crystal and salt diffraction in the protein metal complex

.   Cheers,   Acoot --- Navdeep Sidhu University of Goettingen ---

[ccp4bb] OT: Who's Afraid of Peer Review?

/content/342/6154/60.full Best regards, Navdeep --- Navdeep Sidhu University of Goettingen ---

Re: [ccp4bb] mmCIF as working format?

when you look back at it... --- Navdeep Sidhu University of Goettingen ---

Re: [ccp4bb] popular piece on X-ray crystallography

have said in 1913. But your points would be valuable in rebutting such a view Pete On 19 Apr 2013, at 11:28, Navdeep Sidhu wrote: Dear Pet, On the contrary, far as I know, nature seems to require most solids we see around us to be crystalline. And much of the rest is either

Re: [ccp4bb] popular piece on X-ray crystallography

Institute Department of Molecular Biology Biotechnology University of Sheffield Sheffield S10 2TN ENGLAND --- Navdeep Sidhu Departments of Structural Chemistry Pediatrics II University of Goettingen Office Address: Institute of Inorganic Chemistry Tammannstrasse 4 37077 Goettingen

Re: [ccp4bb] off-topic: special format for multiple sequence (protein) alignment

some of you have seen some programs can do this? Thank you. King regards, Wenhe --- Navdeep Sidhu Department of Structural Chemistry University of Goettingen Tammannstr. 4 37077 Goettingen Germany Email: nsi...@shelx.uni-ac.gwdg.de Phone: +49 551 39 3066 Fax: +49 551 392 2582 Dept. Homepage

Re: [ccp4bb] backbone b-factor

# # bfactor_backbone.gawk # Script to edit PDB file # by Navdeep Sidhu, with thanks to awk information at # http://www.grymoire.com/Unix/Awk.html # # Input: PDB file # Output: 4 columns: 1) Atom name #2) Chain identifier #3) Residue sequence

Re: [ccp4bb] Problem with Rfree and Rfac

A very relevant article: G.J. Kleywegt and T.A. Jones, Model-building and refinement practice, Methods in Enzymology, 277, 208-230 (1997), http://xray.bmc.uu.se/gerard/gmrp/gmrp.html. Sincerely, Navdeep

Re: [ccp4bb] crystallisation

tolerance of glycerol as cryoprotectant. Sincerely, Navdeep --- Navdeep Sidhu Graduate Student University of Saskatchewan --- Quoting sajid akthar [EMAIL PROTECTED]: Dear All My protein size is ~30kD and crystallizes with 19%Peg3350, 0.2M Nacl, and 0.1M Na Cacodylate buffer. Please refer