[ccp4bb] Postdoctoral fellowship in structure-guided drug discovery

Postdoctoral fellowship available in a collaborative structure-guided drug discovery project between my group and groups of Sharon Rossiter and Stewart Kirton at University of Hertfordshire, funded by the Hertfordshire Science Partnership Therapy Accelerator scheme. Successful candidate will

Re: [ccp4bb] coordinate transformation

What I usually do for this is make a copy of the PDB file and change all the atom x-y-z positions to "1.000".  Then I use something like reforigin or my "origins.com" script to shift the original coordinates via allowed symmetry operations, origin shifts, or perhaps indexing ambiguities until

[ccp4bb] Post-Master’s Research Associate

Opportunity Post-Master’s Research Associate Organization Oak Ridge National Laboratory (ORNL) Reference Code ORNL18-07-NSD https://www.zintellect.com/Posting/Details/3817 Academic Levels · Post-Master's Description The Neutron Sciences Directorate (NScD) at Oak Ridge National Laboratory

Re: [ccp4bb] coordinate transformation

I use PISA for the compact molecule construction - it works very well, and probably should be the default at the end of every MR - it also tries to choose a sensible symm op which allows assemblies to be generated easily. But then you would have to think about how to position that assembly as

[ccp4bb] Post Doctoral Structural Biology Position Icahn School of Medicine at Mount Sinai NY

Posted on behalf of a colleague, please respond directly to the e-mail address below. Postdoctoral Position in Structure and Function of G protein-coupled Serotonin Receptors and Neurotransmitter Transporters. A postdoctoral position is available in the research group of Daniel Wacker,

Re: [ccp4bb] Crystal structure of an unknown protein

In this case you know the protein is closely relaed to whatefer contaminer found, and you have good sequence data, so I agree the next step is blast. Maybe it is an isozyme of the structure used. In cases where you solve an unknown by heavy atom derivatives and have no idea what it is; and

Re: [ccp4bb] coordinate transformation

On 12/14/2017 04:34 AM, Tim Gruene wrote: Dear Tommi, 1. if you only need to consider translations, and not other symmetry operations, you can use moleman2, convert coordinates to fractional ones and add or substract the integer that brings the centre of mass closest to 0. 2. In case you

[ccp4bb] ccp4online webservices

Dear All just a heads up that these will be unavailable from 3pm GMT on Friday 15th until the following Monday as we go through fixed line testing on the electrics. Sorry for any inconvenience Charles

Re: [ccp4bb] coordinate transformation

Here is a VERY oldfashioned solution. Find the centre of mass of your molecule. pdbset xyzin mol.pdb end tells you that Make a mini PDB with the CRYST1 record, and two "atoms" - one at 0 0 0, the other at the centre of mass with some atom type say C then distang xyzin min.pdb radi C 20 say

Re: [ccp4bb] Crystal structure of an unknown protein

Wow, pretty cool—you must have solved it to very high resolution to know the sequence from the structure. I cannot imagine, however, how you got this contaminant—maybe phage infection of your bacterial culture? Anyway, I agree with BLAST-ing the sequence, seeing what you get that is closest.

Re: [ccp4bb] Crystal structure of an unknown protein

Hello, Welcome to the club of unexpected results! You don't provide a lot of background, but based on what you wrote you can: 1. Do a BLAST search using a known part of your sequence to find whether this sequence has been deposited. 2. Assign the different residues based on the chemical

[ccp4bb] Crystal structure of an unknown protein

Dear CCP4bb, In 2014, I collected a high quality data set from a crystal. But I could not solve the structure of that crystal because this protein is a contaminate. Recently, I used StruBE's Contaminer and fortunately got the solution. Thanks ContaMiner!!! This protein is a contaminate

Re: [ccp4bb] coordinate transformation

Dear Tommi, if you only need to consider translations, and not other symmetry operations, you can use moleman2, convert coordinates to fractional ones and add or substract the integer that brings the centre of mass closest to 0. In case you want to take the symmetry operations into account,

Re: [ccp4bb] coordinate transformation

Dear Paul, Yes thank you. This was the best answer i think. Someone else already also suggested that also. Coot is very handy indeed. (Would still be curious of knowing how to find the "closest to origin" copy otherwise - but this solves my problem) Thanks to all who responded. Cheers,

[ccp4bb] Scientific programmer vacancy to work with EM validation

Dear all We are part of a consortium which has recently been funded by the Wellcome Trust to develop and disseminate validation tools to assess the quality of cryoEM reconstructions and fitted models. The other members of the project are STFC, Francis Crick Institute, Birkbeck College,