[ccp4bb] Multiple Structural & biophysical roles at GSK R&D, Stevenage, UK

2021-08-06 Thread Chun-wa Chung
Title : Multiple Structural and Biophysical Scientists Roles at GSK R&D, Stevenage,UK. We have multiple openings for talented structural & biophysical scientists to join GSK's UK Structural & Biophysical Sciences group at Stevenage. So if the opportunity to join a multi-disciplinary department t

Re: [ccp4bb] off-topic: structural motif / domain comparison

2021-08-06 Thread Bernhard Rupp
A lesser known service with very powerful search across domains and chains is TopSearch by Manfred Sippl & Cie.: https://topsearch.services.came.sbg.ac.at/ Its training set includes PDB entries up to 2018. Best, BR From: CCP4 bulletin board On Behalf Of Sam Tang Sent: Thursday, Augu

Re: [ccp4bb] off-topic: structural motif / domain comparison

2021-08-06 Thread orly avraham
You might also find use in databases such as pfam, ecod, cath, scop. Orly On Fri, Aug 6, 2021, 09:43 Sam Tang wrote: > Dear all > > Sorry for an off-topic question here. I wonder if anyone may be aware of > any search program which allows one to 'blast' a protein domain just like > we 'blast' a

Re: [ccp4bb] refmac - use weighting term - pdb to mmcif

2021-08-06 Thread Marina Gárdonyi
I deleted a line in the keyword file which was "pdbout format mmcif". It was my first try to convert the pdb file to an mmcif file, but it did not work! Best Marina Zitat von "Krieger, James M" : It could be good to say how you solved it for future users. Best wishes James On Aug 6, 202

Re: [ccp4bb] off-topic: structural motif / domain comparison

2021-08-06 Thread Dalibor Košek
Perhaps DALI can be of use http://ekhidna2.biocenter.helsinki.fi/dali/ Dal. pá 6. 8. 2021 v 8:42 odesílatel Sam Tang napsal: > Dear all > > Sorry for an off-topic question here. I wonder if anyone may be aware of > any search program which allows one to 'blast' a protein domain just like > we '

Re: [ccp4bb] off-topic: structural motif / domain comparison

2021-08-06 Thread Chris Fage
Hi Sam, Perhaps the Modeller service is what you’re looking for? https://salilab.org/modeller/ Best wishes, Chris On Fri, 6 Aug 2021 at 07:42 Sam Tang wrote: > Dear all > > Sorry for an off-topic question here. I wonder if anyone may be aware of > any search program which allows one to 'blas

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

2021-08-06 Thread Rangana Warshamanage
Not sure someone already mentioned these (highly likely) https://www.nature.com/articles/s41586-019-1923-7 https://www.nature.com/articles/s41586-021-03819-2 https://science.sciencemag.org/content/early/2021/07/19/science.abj8754 On Tue, Aug 3, 2021 at 12:53 PM Thorn, Dr. Andrea < andrea.th...@u

Re: [ccp4bb] refmac - use weighting term - pdb to mmcif

2021-08-06 Thread Marina Gárdonyi
Hi, as it is often the case, the mail is out and you are able to solve the problem on your own. Thanks anyway! Best Marina Zitat von Marina Gárdonyi <652c4b26eb10-dmarc-requ...@jiscmail.ac.uk>: Hi, before I will soon finish my PhD, I have to solve one more problem. I managed to refin

[ccp4bb] refmac - use weighting term - pdb to mmcif

2021-08-06 Thread Marina Gárdonyi
Hi, before I will soon finish my PhD, I have to solve one more problem. I managed to refine occupancies and tls in Refmac. I also found out that you can use pdb-extract to convert the pdb file to an mmcif file so that you can validate the structure using the validation server. However, durin