Re: [ccp4bb] xds crashes

Dear Demetres, sounds a bit drastic! The second point alone would certainly suffice, because then no forking is done. What kind of hardware is that? I would expect that on a contemporary workstation you have 8GB of RAM or more; that would allow for 8 or more processes. Do you have a swapfile?

Re: [ccp4bb] xds crashes

Dear Kay, you are right and I do apologize for the misunderstanding. Point 1 and 2 are sufficient. best Demetres On 11/29/2022 10:00 AM, Kay Diederichs wrote: Dear Demetres, sounds a bit drastic! The second point alone would certainly suffice, because then no forking is done. What kind

Re: [ccp4bb] xds crashes

Dear Demetres, On Tue, Nov 29, 2022 at 10:25:17AM +0200, Demetres D. Leonidas wrote: > Dear Kay, > > you are right and I do apologize for the misunderstanding. Point 1 > and 2 are sufficient. You can probably avoid doing any of this by using the LIB= feature of XDS on gzipped CBF files with the

Re: [ccp4bb] Question about CCP4 monomer dictionaries

Hi everyone, Prompted by this discussion I ran a series of CSD conquest searches for peroxide in various environments. CSD conquest makes it easy to perform fairly complex searches (and was used for the Engh & Huber amino acid restraint library for amino acids still extensively used today).

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Re: [ccp4bb] occupancy factors for alternate conformations and alternate ligands

Hi MIke Beyond the obvious that they should sum to no more than unity, if they are similar to or not hugely greater than other temperature factors in your structure, they are probably okay. People often apply restraints or constraints to keep the temperature factors similar for equivalent

Re: [ccp4bb] xds crashes

Dear Kay, many thanks for your suggestions. We will look into this. best Demetres On 11/29/2022 2:35 PM, Kay Diederichs wrote: Dear Demetres, I googled the Ubuntu 22.04 release notes and found https://discourse.ubuntu.com/t/jammy-jellyfish-release-notes/24668 which says "We’ve enabled the

[ccp4bb] AW: [ccp4bb] occupancy factors for alternate conformations and alternate ligands

Hi Mike, My gut feeling is that the accuracy will be around 10%. However it will depend very much how far the two conformation overlap, or not overlap and how good the data is. If there are large non-overlapping regions, accuracy may be better. Best, Herman Von: CCP4 bulletin board Im Auftrag

Re: [ccp4bb] xds crashes

Dear Demetres, I googled the Ubuntu 22.04 release notes and found https://discourse.ubuntu.com/t/jammy-jellyfish-release-notes/24668 which says "We’ve enabled the userspace OOMD service and are shipping the systemd-oomd package by default on the “Ubuntu Desktop” flavour, to avoid overloaded

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