[phenixbb] Error from phenix.find_peaks_holes

[Oleg Sobolev]

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 at 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 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_pro
>> ject/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_pro
>> ject/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_pro
>> ject/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_pro
>> ject/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-onlin
>> e.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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>
>
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