[phenixbb] Error from phenix.find_peaks_holes

[Oleg Sobolev]

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 at 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 at phenix-online.org <phenixbb-bounces at phenix-
> online.org> on behalf of #AHMED TOFAYEL# <TOFAYEL001 at 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?
>
> http://emboj.embopress.org/content/28/6/755
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__emboj.embopress.org_content_28_6_755&d=DgMFAw&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=pvrL1zz81cKSgrwK0o2bLY-9_SY5XnNbJUoV8uk3Vng&s=7SDJ0Xn1Yw2YMcBQKaJp9dCizbRKPrs8YrFvLsfFaJw&e=>
>
> Best regards,
> Tofayel
> NTU Singapore
>
>
>
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