Re: [ccp4bb] Is it possible to fix the position of an atom during real space fitting in Coot?

On 13/03/2018 20:12, Ana Luísa Moreira de Carvalho wrote: You can find the tool “Fixed Atoms” in the Refinement Toolbar (the side menu). Just click Fix Atom and then click the atom(s) you wish to fix. It won’t move in real space refinement or in regularisation. That's right, Ana Luísa. And

Re: [ccp4bb] How to get Imean/SIGImean from separated anomalous data?

Thanks- that works! pdb-redo/tools/cif2cif in.cif out.cif eab On 03/13/2018 05:47 PM, Robbie Joosten wrote: Hi Ed, The pdb-redo program cif2cif does that. I implemented this feature because there was no obvious CCP4 program that did this. You have to have your data in mmCIF format though.

[ccp4bb] release of SPHIRE 1.0

Dear colleagues, We are excited to announce the release of the latest version of our SPHIRE software suite (SPHIRE 1.0) (co-distributed with EMAN 2.21), which is now available from our website: http://sphire.mpg.de Main new components and updates: - SORT3D – A novel 3D

[ccp4bb] release of SPHIRE 1.0

Dear colleagues, We are excited to announce the release of the latest version of our SPHIRE software suite (SPHIRE 1.0) (co-distributed with EMAN 2.21), which is now available from our website: http://sphire.mpg.de Main new components and updates: - SORT3D – A novel 3D

[ccp4bb] How to get Imean/SIGImean from separated anomalous data?

I want to work with an mmcif file that has I+,sigI+,I-,SigI-; in different columns for each reflection (no Imean). cif2mtz gives those same columns in the output mtz, with or without ANOMALOUS keyword. cif2mtz and truncate seem to need the anomalous data as separate reflections hkl and -h-k-l

Re: [ccp4bb] Is it possible to fix the position of an atom during real space fitting in Coot?

You can find the tool “Fixed Atoms” in the Refinement Toolbar (the side menu). Just click Fix Atom and then click the atom(s) you wish to fix. It won’t move in real space refinement or in regularisation. Cheers! > On 13 Mar 2018, at 19:46, Steve Chou wrote: > > Dear Coot

Re: [ccp4bb] Is it possible to fix the position of an atom during real space fitting in Coot?

Yes - you can "FixAtom" - I cant remember which menu it is under - real space rene I think.. Will check tomorrow Eleanor On 13 March 2018 at 19:46, Steve Chou wrote: > Dear Coot developers and CCP4 list subscribers, > > The density of my map is not perfect. However, I

[ccp4bb] Is it possible to fix the position of an atom during real space fitting in Coot?

Dear Coot developers and CCP4 list subscribers, The density of my map is not perfect. However, I know where a specific atom should be located. Every time I did real space fitting, the atom and the associated chemical groups in the whole ligand ran away. Is there a way to fix the position of this

[ccp4bb] University of Oxford - Structural Biology Postdoc position with focus on Drug Discovery - DEADLINE 16/03/18!

The Huber lab at the Structural Genomics Consortium (SGC)/Target Discovery Institute is looking for a highly motivated and enthusiastic postdoctoral fellow to join our team to explore the structure and function of human proteins linked to cancer and inflammatory diseases. Our group is focused

[ccp4bb] Mosaicity histogram in HKL 3000R

Hi Everyone, I am seeing something strange with HKL 3000R with regard to the mosaicity histogram and was wondering if anyone has come across something like it before. From the HKL 2000 manual I understand that the mosaicity histogram should to go through 0 close to 0.5 partiality, to have

[ccp4bb] New SHELX versions and email address

Here is another attempt from my old email address. I was not registered to use the email lists from my new address, but please use it in future! New versions of SHELXE, SHELXL and SHELXT and also Anna Luebben's program pdb2ins that provides a quick way of setting up a shelxl refinement given a

[ccp4bb] PhD positions in structural biology at EMBL Grenoble

Dear colleagues, I would like to inform you about the ongoing call for applications to the EMBL International PhD programme. In particular, I would like to draw your attention to several open PhD positions in the area of structural biology at EMBL Grenoble. The EMBL international PhD

Re: [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone crystal?

Dear Joseph, I fully agree with Daniel Himmel's answer but you might be able to "index" your reflections and get a approximate cell parameters. I did that in the past with crystals that diffracted very poorly up to 15 angst. I used HKL200 at that time, cheated with the distance (HKL2000 won't

[ccp4bb] Joint Liverpool/Diamond PhD studentship

Dear all, A fully-funded 4-year PhD studentship, joint between the University of Liverpool and the Diamond Light Source, is now available. Paying an enhanced stipend, it involves application of computational methods to characterise and solve diffraction datasets from crystals of transmembrane

[ccp4bb] Postdoctoral Research Fellow vacancy - protein kinases in Bayliss lab, Leeds

I am looking for a Postdoctoral Research Fellow to explore the regulation of protein kinases and to contribute structural insights to drug discovery projects. The catalytic activities of protein kinases are controlled through protein-protein interactions and post-translational modifications.

Re: [ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

On 13/03/2018 07:36, M T wrote: So finally the solution was easy access... Thanks to someone who suggest me to do that, I created a new user, to verify if coot was ok under that session, and it was fine. Then I went back on my session, I removed the files below: 0-coot-history.py

Re: [ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

So finally the solution was easy access... Thanks to someone who suggest me to do that, I created a new user, to verify if coot was ok under that session, and it was fine. Then I went back on my session, I removed the files below: 0-coot-history.py 0-coot-history.scm 0-coot.state.py

[ccp4bb] Vacancies@EMBL Hamburg Unit

Dear all, I would like to draw your attention to the following vacancy notices@EMBL Hamburg: *Scientific Technical Officer* - Platform for Integrated Structural Biology at EMBL/CSSB http://s.embl.org/HH00138 *Postdoctoral Fellowship* - Integrated Structural Biology of Peroxisomal