Hi Reza,

Thank you for sharing files and letting us fix it. The fix will be available in nightly builds from dev-2748 and higher. Meanwhile I uploaded the results of fixed command to the folder you shared with me.

Best regards,
Oleg Sobolev. 

On Mon, Apr 17, 2017 at 9:18 AM, Oleg Sobolev <osobolev@lbl.gov> wrote:
Hi Reza,

I'm afraid this needs to be fixed on our end. Can you please send me (off list) the files you used for this run?

Best regards,
Oleg Sobolev.

On Mon, Apr 17, 2017 at 4:34 AM, Reza Khayat <rkhayat@ccny.cuny.edu> wrote:

Hi,


I'm getting the following error when running phenix.find_peaks_holes


peak=   -3.937 closest distance to pdb=" CB  ASPCB 228 " =    2.259
peak=   -3.521 closest distance to pdb=" O   PROCB 229 " =    2.275
peak=   -4.264 closest distance to pdb=" CD1 LEUCB 231 " =    4.718
peak=   -3.384 closest distance to pdb=" CD1 LEUCB 231 " =    5.050

Traceback (most recent call last):
  File "/opt/X-tal_suite/phenix-dev-2733/build/../modules/cctbx_project/mmtbx/command_line/find_peaks_holes.py", line 550, in <module>

SUMMARY OF MAP PEAKS:
  mFo-DFc >  3:  10775
  mFo-DFc >  6:    847
  mFo-DFc >  9:     42
  mFo-DFc max:   13.04
  mFo-DFc < -3:   6148
  mFo-DFc < -6:    525
  mFo-DFc < -9:     49
  mFo-DFc min:  -10.40


    run(sys.argv[1:])
  File "/opt/X-tal_suite/phenix-dev-2733/build/../modules/cctbx_project/mmtbx/command_line/find_peaks_holes.py", line 511, in run
    result.save_pdb_file(file_name="%s.pdb" % prefix, log=out)
  File "/opt/X-tal_suite/phenix-dev-2733/build/../modules/cctbx_project/mmtbx/command_line/find_peaks_holes.py", line 173, in save_pdb_file
    rg = create_atom(xyz, peak, k)
  File "/opt/X-tal_suite/phenix-dev-2733/build/../modules/cctbx_project/mmtbx/command_line/find_peaks_holes.py", line 159, in create_atom
    rg = iotbx.pdb.hierarchy.residue_group(resseq=str(serial))
ValueError: string is too long for target variable (maximum length is 4 characters, 5 given).

Is it referring to the 5 characters used for the residue name? If so, how do I correct for this? This is a PDB of a virus (60 subunits). Thanks.


Best wishes,
Reza


Reza Khayat, PhD
Assistant Professor 
City College of New York
Department of Chemistry
New York, NY 10031
From: phenixbb-bounces@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of #AHMED TOFAYEL# <TOFAYEL001@e.ntu.edu.sg>
Sent: Monday, April 17, 2017 12:38 AM
To: PHENIX user mailing list
Subject: [phenixbb] Generate a map showing local agreement between map and model
 

Dear developers and users,

Is it possible to generate a map to show local agreement between cryo-EM map and the model generated using the same map? If I am not wrong, the supplementary figure S5 had accomplished the job (using Chimera), but I don't understand how to generate a similar figure for my project. Is it possible to do with phenix?

Best regards,
Tofayel
NTU Singapore



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