Dear Xin,
I can see that your input model is from Buccaneer. I would just like to
note that there has been recently done a lot of development in the
program ModelCraft. It is now recommended to use ModelCraft (available
in CCP4i2 or CCP4Cloud) rather than Buccaneer.
If I were you, I would also try MrParse in CCP4 or 'Predict and Build:
Crystallography' in Phenix for molecular replacement. These programs are
very powerful. The input are only the diffraction data and a sequence;
models for molecular replacement are prepared automatically from PDB
entries and AlphaFold predictions. It may solve your problems relating
to the long poly-ala sequnces in your current structure model.
Best regards,
Martin
On 24/09/2024 08:35, zx2...@connect.hku.hk wrote:
Dear Kay,
Thank you for your reminder. I am encountering the following error
messages:
Sorry, the segment 'AAAAAAAAAAAAAAAAAAAA' (residues 1:20 of chain 'D')
could not be matched
to sequence. Matching is required for rebuild_in_place.
You might try supplying a different 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 <CCP4BB@JISCMAIL.AC.UK> on behalf of
zx2...@connect.hku.hk <zx2...@connect.hku.hk>
*Sent:* 23 September 2024 09:13
*To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
*Subject:* [ccp4bb] Phenix.autobuild command problem
*This is an external email.*
Dear all,
I encountered an issue while running the following command with the
attached files:
BUCCANEER.pdb
<https://connecthkuhk-my.sharepoint.com/:u:/g/personal/zx2020_connect_hku_hk/EaiKgmMxOS1Lg9BUIkXYdQcBbM3wshv-ZR1q5ssPpY5bJA>
PHASER.1.mtz
<https://connecthkuhk-my.sharepoint.com/:u:/g/personal/zx2020_connect_hku_hk/EcGf62NLnX9CmB-TGKn3_-gBKNsv7n-6ipzESzOWAyQR6Q>
phenix.autobuild data=PHASER.1.mtz model=BUCCANEER.pdb
The error message I received was:
Interestingly, this error does not occur when I use the Phenix GUI
with the default autobuild configuration.
Could anyone help me troubleshoot this command line issue?
Thank you very much!
Best regards,
Xin
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