Phenix Ligand Identification error
Dear All Greetings I was searching for a ligand present in the active site of my protein using Ligand Search in "PHENIX" but i stuck in between with an error : A Python error was detected. This may be a problem with the program settings, an error in your data, or a bug; click "OK" to send a bug report to the PHENIX developers. AttributeError : ligand_identification instance has no attribute 'connections' Traceback: File "/home/programs/linux/phenix- 1.6.1-357/cctbx_project/libtbx/thread_utils.py", line 137, in run return_value = self._target(self._args, self._kwargs, self._c) File "/home/programs/linux/phenix-1.6.1-357/cctbx_project/libtbx/runtime_utils.py", line 55, in __call__ result = self.target() File "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py", line 1769, in __call__ identify_ligands = ligand_identification(args=list(self.args), quiet=False) File "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py", line 308, in __init__ ligand_identification.Run(self, params) File "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py", line 1454, in Run return self.connections['STOP '] I am not able to identify the problem? Please let me know if some one can identify the problem, i don't know whether it is a bug or problem in my files. Thanks for your suggestions in advance. Rajan -- ************************************************ Current Address: Rajan Vyas Research Scholar Deptt. of Biotechnology Panjab University Chandigarh, India 160014 Mob. +919417374197 Fax: +91-172-2625254 ************************************************
On Sat, Apr 24, 2010 at 3:19 AM, Rajan
I was searching for a ligand present in the active site of my protein using Ligand Search in "PHENIX"
but i stuck in between with an error :
AttributeError : ligand_identification instance has no attribute 'connections' File "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py", line 1454, in Run return self.connections['STOP ']
Please let me know if some one can identify the problem, i don't know whether it is a bug or problem in my files.
Possibly both. The error message is definitely a bug - I'll make sure the appropriate person gets this. It may have already been fixed, because the most current code is obviously different than what's in 1.6.1, so it might be worth trying the latest nightly build. I just put last night's installer online; it should be relatively stable. However, the reason it stopped at that point in the code was possible an input problem: print 'Resolve failed to make difference map in Step 1.\n' print '!!!!!Please double-check mtz labin assignment.!!!!!\n' So it might not be able to use the data you're providing it - impossible to tell why from here. -Nat
Hi Rajan, If you are using the command-line, could you send me your full input command, and possibly the log file of this particular job? Also, it would be better if you can send me your mtz file. You can send those to me off-line if you like. Thanks, Li-Wei Hung Rajan wrote:
Dear All
Greetings
I was searching for a ligand present in the active site of my protein using Ligand Search in "PHENIX"
but i stuck in between with an error :
A Python error was detected. This may be a problem with the program settings, an error in your data, or a bug; click "OK" to send a bug report to the PHENIX developers.
AttributeError : ligand_identification instance has no attribute 'connections' Traceback: File "/home/programs/linux/phenix- 1.6.1-357/cctbx_project/libtbx/thread_utils.py", line 137, in run return_value = self._target(self._args, self._kwargs, self._c)
File "/home/programs/linux/phenix-1.6.1-357/cctbx_project/libtbx/runtime_utils.py", line 55, in __call__ result = self.target()
File "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py", line 1769, in __call__ identify_ligands = ligand_identification(args=list(self.args), quiet=False)
File "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py", line 308, in __init__ ligand_identification.Run(self, params)
File "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py", line 1454, in Run return self.connections['STOP ']
I am not able to identify the problem?
Please let me know if some one can identify the problem, i don't know whether it is a bug or problem in my files.
Thanks for your suggestions in advance.
Rajan
-- ************************************************ Current Address:
Rajan Vyas Research Scholar Deptt. of Biotechnology Panjab University Chandigarh, India 160014 Mob. +919417374197 Fax: +91-172-2625254 ************************************************
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Dear phenixbb, i have a protein on which a cysteine has been modified and I can't find a way to refine my structure with it. this seams like a fairly easy problem as a lot of people are refining structures with post-translational modifications, but i can't find the info on how to do it. Could someone point me to a web page explaining it? If i understand correctly, i have to create the modified residue, create the restraints, and define it as a L-peptide. Is that correct? thanks a lot vincent -- Vincent Chaptal Dept. of Physiology at UCLA http://www.physiology.ucla.edu/Labs/Abramson/index.html http://www.physiology.ucla.edu/Labs/Abramson/index.html/ Phone: 1-310-206-1399 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
Vincent
You can run ReadySet! thus
phenix.ready_set model.pdb
to, among other things, generate a restraints file for any
non-standard residues. Simply pass this to phenix.refine.
Nigel
On Thu, May 13, 2010 at 11:36 AM, vincent Chaptal
Dear phenixbb,
i have a protein on which a cysteine has been modified and I can't find a way to refine my structure with it. this seams like a fairly easy problem as a lot of people are refining structures with post-translational modifications, but i can't find the info on how to do it. Could someone point me to a web page explaining it?
If i understand correctly, i have to create the modified residue, create the restraints, and define it as a L-peptide. Is that correct? thanks a lot vincent
--
Vincent Chaptal
Dept. of Physiology at UCLA
http://www.physiology.ucla.edu/Labs/Abramson/index.html http://www.physiology.ucla.edu/Labs/Abramson/index.html/
Phone: 1-310-206-1399
IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov
participants (5)
-
Li-Wei Hung -
Nathaniel Echols -
Nigel Moriarty -
Rajan -
vincent Chaptal