[ccp4bb] i2run ProvideAsuContents Problem

To whom it may concern, I am currently working with CCP4 version 8.0.016 on an Ubuntu 22.04 system. In my efforts to follow the guidelines provided in the documentation (https://ccp4i2.gitlab.io/rstdocs/i2run/i2run.html), I have encountered an issue. Specifically, I have encountered a problem w

Re: [ccp4bb] Coot SSM Superpose Problem

Dear all, Following the advice provided by Paul and Yi Min, the "Symm Shift Reference Chain Here" function has proven successful! I am deeply grateful for your guidance. Best regards, Xin ____ From: zx2...@connect.hku.hk Sent: 16 February 2024 17:26 To: P

Re: [ccp4bb] i2run crank2 problem

with the scripting question, but it solved easily from the I2 interface? This is run on a Mac. CRANK2 called SHELX - found SE with weak signal.. Some difference between hand It traced ALA - R factor 41% Then BUCCANEER or MODELFIR quickly built and sequenced the rest.. Eleanor On Thu, 15 Feb

[ccp4bb] Running Crank2 via Command Line

Hello everyone, I'm reaching out to inquire if anyone has experience with executing Crank2 through the command line. I attempted utilizing the crank command, but it appears an XML input is required. To generate the XML file, I employed gcx with the following parameters: gcx SEQIN /mnt/ssd/SAD/

[ccp4bb] CCP49.0 i2run problem

Hi all, I am experiencing some issues with i2run command after updating CCP4 to version 9.0. The command I used is as follows: $CCP4/lib/python3.9/site-packages/ccp4i2/bin/i2run ProvideAsuContents \   --ASU_CONTENT \ sequence=${sequence} \    nCopies=1 \    polymerType=PROTEIN \    

[ccp4bb] Phenix.autobuild command problem

Dear all, I encountered an issue while running the following command with the attached files: [https://res.public.onecdn.static.microsoft/assets/mail/file-icon/png/generic_16x16.png]BUCCANEER.pdb

Re: [ccp4bb] Phenix.autobuild command problem

sequence file or no sequence file I have also attached the log file for your reference. Thank you very much for your assistance. Best regards, Xin From: CCP4 bulletin board on behalf of zx2...@connect.hku.hk Sent: 23 September 2024 09:13 To: CCP4BB@JISCMAIL.AC.

[ccp4bb] Question about Phaser rotation and translation search parameters

Dear All, I hope this email finds you well. I would like to clarify how the Phaser program determines the search range and step size for both the rotation and translation searches. Specifically, I am wondering: 1. Rotation search range: What are the typical angular ranges for α, β, and γ? Fo

[ccp4bb] How to Obtain the PAE Matrix from Local AlphaFold Predictions

Hi everyone, I’m currently working with a locally deployed version of AlphaFold (monomer) and was wondering if anyone knows how to obtain the PAE matrix from files in the predicted folder. Any guidance or suggestions would be greatly appreciated. Thank you in advance for your help! Best regard