Hello everyone!
I used Schrodinger Prime to predict a protein structure (sequence identity with template ~71%). Knowledge-based model building method was used to generate the output model.
While validating the output models (before and after loop refinement) on ProSA, its returning an error like "Z-Score/Energy plot: not calculated. Please check if the selected chain id matches a protein chain!"
Can someone help me to get rid of this error?
Thanks!
P.S: Although I have modelled the same protein using RaptorX, and its output is returning without any errors on ProSA.
Hey Julia Bezerra ,
When you export your PDB structure, try unchecking the 1st PDB option which says "write SEQRES, HELIX, SHEET, TURN, and SSBOND information".
Hope this will solve your issue.
Lemme know if you need any other help.
Hey Puneet Kumar , thank you for your help!
Since the default was the box unchecked , I tried check it.
And it worked!
Thank you again!@
Hey there, do any of you guys now how to run DOPE assessment on modeller? Im not quite sure how to interpret the command from the website:
(https://salilab.org/modeller/8v1/manual/node155.html ).
Your help will truly be appreciated
Puneet Kumar , Suraj Raju , SAMEE ULLAH
, Martiniano Bello
Mbalenhle Mfeka Sorry , i never used modeller. I basically use I-TASSER for homology modelling followed by Modrefiner Or Phyre2 then refine with 3D refine and Galaxy refine.
2. Perform Ramachandran plot analysis by RAMPAGE server. download PS file convert to PDF.
3. Check ERRAT, QMEAN, PROVE scores .
4. Perform either ProSa analysis to get Z-score or verify 3D.
Hope this helps. :)
Vijaya Sai Ayyagari
, open the PDB file in a text editor and check for any non-standard formatting/content.
Hi Puneet Kumar
I face the same problem mentioned by you earlier with ProSA-web.
Your suggested solution was not clear for me.
Could you clarify how to solve the problem?
"When you export your PDB structure, try unchecking the 1st PDB option which says "write SEQRES, HELIX, SHEET, TURN, and SSBOND information"." where I can do this? In any program or software?
Thanks in advance,
Regards
Sarah Tb Please check the attached file. Now it is working fine with ProSA-web.
Hello SAMEE ULLAH
, faced the same issue as shown and used your hack to solve it. Saving the molecule and writing a segment identifier in PyMol created the new pdb file that I used for its ProSA
Sarah Tb Please find the attached file.
Sorry for the delayed response.
Hii, Puneet Kumar
I am facing the same issue as you were. Can you please correct the attached model so that I can proceed further?
If you can help in this regard, kindly share your tricks to my SMS box for using the ProSA server in a smooth way. @
Thank you.
You can also use AutoDock tools (ADT). Open your pdb file with ADT, add hydrogens, and save it again (write pdb with ADT).
This method worked for me
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