Re: [phenixbb] Error from phenix.find_peaks_holes

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 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 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:* [email protected] on behalf of #AHMED TOFAYEL# *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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