[phenixbb] Re: phenixbb Digest, Vol 237, Issue 1 (out of office)

Thank you for your e-mail. I am out of office until September 15th, 2025. I will respond to your e-mail as soon as possible upon my return. For urgent matters please contact: [email protected] Thank you for your understanding. With kind regards, Elisabeth Laurent

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Send phenixbb mailing list submissions to [email protected] To subscribe or unsubscribe via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. atom selection for elements anisotropic rest TLS (Georg Mlynek) 2. Re: atom selection for elements anisotropic rest TLS (John Bacik) 3. adding together (James Holton) 4. Re: adding together (Petrus Zwart) ---------------------------------------------------------------------- Message: 1 Date: Wed, 10 Sep 2025 08:17:54 +0200 From: Georg Mlynek Subject: [phenixbb] atom selection for elements anisotropic rest TLS To: "[email protected]" Message-ID: <[email protected]> Content-Type: text/plain; charset=UTF-8; format=flowed Dear scientific community, I ticked TLS parameters in Strategy and in Selection Editor I choose 1 group/chain. Then under Anisotropy elements I typed: element Mn or element Mg Running this throws the error: Bad (empty or mixed) selection in adp_individual_iso. What would be the right input under Isotropic atoms so the TLS is not mixed up. Many thanks, br Georg. ------------------------------ Message: 2 Date: Wed, 10 Sep 2025 18:38:38 +0000 (UTC) From: John Bacik Subject: [phenixbb] Re: atom selection for elements anisotropic rest TLS To: "[email protected]" , Georg Mlynek Message-ID: <[email protected]> Content-Type: text/plain; charset=UTF-8 Hi Georg, if you are trying to refine anisotropic B-factors for a Mn or Mg element only I do not think you need TLS parameters for that. One way to refine specific elements would be in Refinement settings/Modify start model/B-factors/tick "Convert to anisotropic" and select for the Mn or Mg element. Any element that is formatted as anisotropic will remain so through subsequent rounds of refinement. All the best,John On Wednesday, September 10, 2025 at 01:18:06 AM CDT, Georg Mlynek wrote: Dear scientific community, I ticked TLS parameters in Strategy and in Selection Editor I choose 1 group/chain. Then under Anisotropy elements I typed: element Mn or element Mg Running this throws the error: Bad (empty or mixed) selection in adp_individual_iso. What would be the right input under Isotropic atoms so the TLS is not mixed up. Many thanks, br Georg. _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s ------------------------------ Message: 3 Date: Fri, 12 Sep 2025 11:28:47 -0700 From: James Holton Subject: [phenixbb] adding together To: PHENIX user mailing list Message-ID: Content-Type: text/plain; charset=UTF-8; format=flowed Greetings Phenix developers! I have what I hope is a quick question. I'm trying to add a stack of phased structure factors together. Specifically from separate runs of phenix.fmodel. Normally, I'd use sftools for this, but the distributed version has a size limitation. According to Tom's phenix chatbot, I can use phenix.maps for adding two sets of structure factors togetheiotbx.reflection_file_editor, but it only works from the GUI (and I want to add 1000 mtz files together). phenix.xmanip looks promising too, but again, seems to want a pdb and an mtz. Is there a recommended way to do this? I've already asked this on CCP4BB, but I wanted to get the Phenix take on these kinds of manipulations. Thank you, -James Holton MAD Scientist ------------------------------ Message: 4 Date: Fri, 12 Sep 2025 11:34:35 -0700 From: Petrus Zwart Subject: [phenixbb] Re: adding together To: James Holton Cc: PHENIX user mailing list Message-ID: Content-Type: text/plain; charset="UTF-8" https://claude.ai/public/artifacts/f390c669-b8c7-4776-a4bc-1761b110bba0 On Fri, Sep 12, 2025 at 11:29 AM James Holton wrote:

Greetings Phenix developers!

I have what I hope is a quick question. I'm trying to add a stack of phased structure factors together. Specifically from separate runs of phenix.fmodel. Normally, I'd use sftools for this, but the distributed version has a size limitation. According to Tom's phenix chatbot, I can use phenix.maps for adding two sets of structure factors together, but it seems to only want to combine an mtz with a pdb. There is iotbx.reflection_file_editor, but it only works from the GUI (and I want to add 1000 mtz files together). phenix.xmanip looks promising too, but again, seems to want a pdb and an mtz. Is there a recommended way to do this?

I've already asked this on CCP4BB, but I wanted to get the Phenix take on these kinds of manipulations.

Thank you,

-James Holton MAD Scientist

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-- ------------------------------------------------------------------------------------------ Peter Zwart Staff Scientist, Molecular Biophysics and Integrated Bioimaging Berkeley Synchrotron Infrared Structural Biology Biosciences Lead, Center for Advanced Mathematics for Energy Research Applications Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 ------------------------------------------------------------------------------------------ ------------------------------ Subject: Digest Footer _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] ------------------------------ End of phenixbb Digest, Vol 237, Issue 1 ****************************************