March 2026 - cctbxbb - phenix-online.org

electron density value near an atom
by robert＠oeffner.net 06 Jun '26

06 Jun '26

Dear CCTBX users/developers I would like to calculate the theoretical electron density value at a point in space as a function of an atom specified by its coordinate and its form factor. I’ll assume it’s for a certain X-ray wavelength, say 1.0Å. If someone would have the time to give me a few pointers on how to do this using the CCTBX I'd be very grateful. Thanks in advance, Rob

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chiral validation
by James Holton 06 Jun '26

06 Jun '26

Can anyone tell me the units of the numbers being displayed by phenix.chiral_validation? The --help documentation doesn't mention anything about chirality. Seems to be a copy of the documentation for omegalyze? Just thought that might be of interest, and I also want to know what the numbers mean. Cheers, -James

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cluster coordinates to asymmetric unit
by robert＠oeffner.net 06 Jun '26

06 Jun '26

Hi, I'm trying to work out how to cluster atomic coordinates into one asymmetric unit in a crystal for a given spacegroup rather than the atomic coordinates placed in arbitrary asymmetric unit copies in the unit cell. I think the tools to be used must be in cctbx.crystal.direct_space_asu and I have been trying but failed to understand how the test tst_crystal_asu_clusters.py works. Is there already a phenix or cctbx program that can do this? Many thanks, Robert

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atomic density profile at finite resolution
by robert＠oeffner.net 06 Jun '26

06 Jun '26

I came across this article https://doi.org/10.1107/S160057672201144X. Although I have yet to read it in details I wonder if the CCTBX can Fcalc maps at finite resolution, i.e. not using Gaussian atomic density profiles. It looks like the function in cctbx.maptbx.atom_curves.bcr_approx(...) is suited to do so. If so, how would I use this for generating a real space map as in https://cci.lbl.gov/docs/cctbx/script_1/#create-a-map-from-a-pdb-file but now using atomic density profiles at finite resolution? Many thanks, Robert

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getting indices of selected grid elements of a map
by robert＠oeffner.net 06 Jun '26

06 Jun '26

Hi, I am wondering if there is an efficient way to retrieve the 3D indices of a selection from a map. In the example on https://cci.lbl.gov/docs/cctbx/doc_low_flex_advanced/#getting-indices-of-se… it is shown how to list the indices of a subset of grid elements of the map as in print(list(isel)) But isel is a 1D representation of 3d map indices. What if I want to get hold of the list of 3D indices corresponding to the indices in the isel array? Is there a fast boost-python way of doing this or would I have to do a 3D loop over the unit cell grid numbers to see if enumerated grid elements matches any of the elements in the isel array? Many thanks, Rob

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reduce2 and cell construction from python script
by Enrico Ravera 06 Jun '26

06 Jun '26

Hi, I apologize for the naive post. I am trying to figure out how to perform the following tasks: 1) read in a mmcif file (which I think I can do following the tutorial); 2) trim the solvent and hydrogen atoms (probably I can do it following the tutorial); 3) run reduce2 to get hydrogens in the nuclear positions (no clue); 4) get the full content of the unit cell (no clue). Any help is appreciated. All the best, Enrico

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API question
by robert＠oeffner.net 30 Mar '26

30 Mar '26

Hi, As far as I know variables produced with CCTBX in python that come out as flex arrays can be converted to numpy with a function, as_numpy_array(), that is a member of flex_array variables. I am wondering if there are methods for doing the reverse in CCTBX. Probably not difficult to write a python loop for a specific case. But more generally? Many thanks, Rob

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Jerome Powell
by Son Kenneth 06 Mar '26

06 Mar '26

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Jerome Powell
by Son Kenneth 06 Mar '26

06 Mar '26

Hello, Greetings how're you I'm Jerome Powell from Washington DC United States 🇺🇲 . .. Good morning This Bank Of America Address: 3401 Connecticut Ave NW, Washington, DC 20008, United States Department: ATM card payment Federal How could you keep trusting people and at the end you will loose your hard earned money,or are you being deceived by their Fake names? They impersonate on many offices claiming to be the first lady JOE BIDDEN/ FBI one Office or the other.President Joe Biden United States • upresidentjoebiden(a)gmail.com Their game plan is only just to extort your hard earned money.And We Receive Information From Federal Republic of Benin Republic information Agency Clerk In Benin Republic YOU have been sending money to Benin Republic in order to receive your fund up till now You have not receive any dime rather they keep asking you for more money. ceochiefexecutiveofficermoynih(a)gmail.com You are receiving this email from This Rev bergoglio Jorge Mario the Rev Agent of Bank of America, and am writing to inform you that your payment which you have been struggling to receive has been approved and endorsed by the United Nation Organization authorities, minternationalimf(a)gmail.com Your details information has been confirmed with the instruction and approvals given from International Monetary Fund and Federal Bureau Investigation (FBI, Washington DC, USA regards The sum of US$90.,5000,000.00 which was deposited in our bank, and we have been instructed to pay you directly via personal ATM card The Management has resolved to open Personal ATM card Account for you with our bank and then give you the on-line access which will enable you to check and make withdrawal, transfer out to any part of the world of your choice with your ATM card. Jerome Powell321 • jeromepowell312hayden(a)gmail.com We are going to have this ATM card account open on your name as soon as you reply to this important e-mail and give you your new open account information’s for your record.Once we show you prove of fund by giving you the new Personal ATM Account and your real account balance of US$90.5,00,000.00 which is your full payment of the full amount credited to your ATM card We are only given you the benefit of doubt by agreeing in showing you that we are capable of opening the new ATM account on your behalf and give you the full withdrawal and transfer access for your record.Let me know that you agree and understand the important of this matter before we go Federal ReserveBank • rfederal84(a)gmail.com ahead and get this matter completed for you because we are professional in handling international matters like this. Kindly Send the Above information to enable us set the ATM account open for you. First Name : Last Name: State of Origin: Nationality: Phone: Marital Status: Gender: Date of Birth: Residential Address: City: State: Country: ZIP/Postal Code: Office Address: E-mail:Please, reconfirm your direct cell phone number to enable voice communication Looking forward for your next letter Thank you for your patient. PLEASE SEND YOUR NAME AS IT IS CLEARLY WRITTEN IN YOUR PASSPORT AND ID CARDS SO THAT WE WILL NOT MAKE MISTAKE. Regards Donald John Trump's • donaldjohntrumps94(a)gmail.com call or text krissymarshall1989(a)gmail.com As you read this may the peace of Almighty be with you.

1 0

Re: coot help
by 余雅梅 04 Mar '26

04 Mar '26

Thank you all. I'll try coot 1. Yamei > -----Original Messages----- > From: "Paul Emsley" <pemsley(a)mrc-lmb.cam.ac.uk> > Send time:Thursday, 03/05/2026 06:14:59 > To: "Pavel Afonine" <pafonine(a)lbl.gov>, "cctbx mailing list" <cctbxbb(a)phenix-online.org>, 余雅梅 <yamei_yu(a)scu.edu.cn> > Subject: Re: [cctbxbb] coot help > > Hello Yamei, > > (Thank you Pavel) > > Depends what you mean by "resolve." > > In the plane sense of the word, probably the best thing you could do is > keep throwing money at the XQuartz developers until they fix the issue. > Until then Coot 0.9.x is dead on macOS Tahoe. > > If, by "resolve" you mean "work-around" or "alternative" then Coot 1 is > the answer. > > There is a good chance that by the end of the month, Coot 1 and the > Phenix gui will work nicely together (if they don't already). > > Paul. > > On 04/03/2026 17:20, Pavel Afonine wrote: > > > > Hi Yamei, > > > > This isn’t the most appropriate mailing list for your question. This > > topic has been discussed extensively on ccp4bb. What you explain rings > > the bell. Search ccp4bb archives -- the conversation was somewhere > > around past month. > > > > Pavel > > > > On 3/3/26 18:25, 余雅梅 wrote: > >> Dear colleges, > >> > >> I recently upgraded my system to macOS Tahoe Version 26.2 before > >> noticing the warning: "Important: Do not upgrade to macOS Tahoe if > >> you are using COOT 0.9. XQuartz fix is not yet available." Now COOT > >> is no longer functional on my machine. Could anyone advise on how to > >> resolve this issue? > >> > >> Thank you so much! > >> > >> All the best! > >> > >> Yamei!

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