[ccp4bb] Unable to access my old projects in new installed ccp4

Hi, I have uninstalled ccp4 from my laptop and reinstalled a recent version. I am unable to access my old run and also my project directory looks empty. I am able to individually connect to each project. Since I have multiple projects is there a way to connect all my project at once Thanking y

Re: [ccp4bb] Which version of ccp4 introduced i2run and/or where does it live?

Hi Maggie, I have CCP4 version 8.0 on my Mac and it does have the file /Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ccp4i2/bin/i2run If I run it without arguments, it says CCP4 /Applications/ccp4-8.0 ccp4i2 version 1.1.0 ccp4i2 source revision 6539 F

Re: [ccp4bb] [External] [ccp4bb] Off topic : plasmid expression vector for E.Coli with a cleavable his-tag at the c-ter

Dear all, thank you for your valuable suggestions. Have a good day, Flavio. Il 16/02/24 15:36, Karla J. F. Satchell ha scritto: Sorry did not mean to go off topic. Original question was requests for suggestions of cleavable c-term tag vectors. I only meant to provide info on one type recomme

Re: [ccp4bb] [off topic] Recovering pET expression plasmid from BL21 strain

Hi Javier, For a few years (during an industry job) we regularly cloned directly into BL21 (we made our own high competency cells) and confirmed via expression before plasmid sequencing. Only after sequencing did we transform into a cloning strain for miniprep and “long term storage”. We didn’t s

Re: [ccp4bb] Which version of ccp4 introduced i2run and/or where does it live?

Hi Kay, I did find /Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/site-packages/ccp4i2/bin/i2run on my Mac, and was able to use that to successfully bring up the import_merged help documentation, so I think that's working - thanks! For general reference, thanks to an individu

[ccp4bb] CBMS Lecture Series - Olga Rechkoblit - February 21st, 13:30 (EST)

You are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. Olga Rechkoblit Mount Sinai School of Medicine WEDNESDAY, February 21, 13:30 (EST) "Activation of bacterial immune system by cyclic nucleotides" Register in advance for this meeting: h

[ccp4bb] Use a Python Package to Access the RCSB PDB Search API

RCSB PDB now maintains a Python package that can be used for accessing our Search API, rcsbsearchapi (https://rcsbsearchapi.readthedocs.io/en/latest/index.html). The package can be installed from PyPI or by downloading the source code on GitHub (https://github.com/rcsb/py-rcsbsearchapi). This r

[ccp4bb] Computational Instrument Scientist - Biology

We are seeking a Computational Instrument Scientist (CIS) for small-angle neutron scattering (SANS). This position resides in the Neutron Scattering Division (NSD) at Oak Ridge National Laboratory (ORNL). Applications are sought from highly creative and motivated individuals with demonstrated s

[ccp4bb] Difficult Molecular replacement

Hello all, I recently collected data on some plate crystals for a previously uncharacterized protein at the ALS light source. The XDS auto-data processing log output indicates that my resolution is 2.8 angstroms. The protein is a helicase with homologs already in the protein data bank making it

Re: [ccp4bb] Difficult Molecular replacement

Hello Marco, This may seem a little obvious, but did you check the sequence of your protein from the gel/ crystals? I've found mass spec to be very useful in this regard as we've had at least two instances of having a protein that looked to be the right size/ correct protein, but wasn't after m

Re: [ccp4bb] Difficult Molecular replacement

Hello Marco, First: compare your unit cell parameters with RCSB (there is an option for that in the search, very helpful). Give it say 5% error margin. Worst case scenario - cry a little, having found that your protein is something else... Next, check in depth for space group oddities, twinning,

Re: [ccp4bb] Difficult Molecular replacement

Hello Marc- My first thought is do you have the correct space group? Are you searching for other space groups in the point group? Second, helicases are multimers, but the orientation of the monomers that make up the multimers may deviate significantly. If you didn't use a monomer, it's worth do

Re: [ccp4bb] Difficult Molecular replacement

Hello Todd, I get the best solution for p22121 space group after MR with an LLG score of 640 from phaser. and the Rfree is .4748. However after MR refinement does not lower the Rfree and it appears to make the Rfree worse. The XDS software indicates that my best solution is P21 21 2. Often Phase

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Difficult Molecular replacement

Hello Marco, I also feel that it might be due to the wrong space group because all the homologous models and alphafold model did not improve the R values. Make sure that you turn on “All possible in same pointgroup” when you run Phenix.Phaser-MR. I work with P212121 crystals a lot. Sometimes, i