MSTA issue

[hduar008]

I'm trying to run USalign locally but I keep getting this error:

@MacBook-Pro-6 dino_models % USalign -dir dino_models/ input_list -suffix .pdb -mm 4
Warning! Cannot parse file: dino_models/ALEFU_ABO47877_HLP.pdb. Chain number 0.
Warning! Cannot parse file: dino_models/BREMI_REEF_HLP.pdb. Chain number 0.
Warning! Cannot parse file: dino_models/CRYCO_Q39474_HCC.pdb. Chain number 0.
Warning! Cannot parse file: dino_models/KARVE_ABV22220_HLP.pdb. Chain number 0.
Warning! Cannot parse file: dino_models/LINPO_Q84U55_HLP.pdb. Chain number 0.
Warning! Cannot parse file: dino_models/PFIPI_ABI14231_HLP.pdb. Chain number 0.
Warning! Cannot parse file: dino_models/POLGL_CAE8636195_HLP.pdb. Chain number 0.
Warning! Cannot parse file: dino_models/PROMI_Q6YND9_HLP.pdb. Chain number 0.
Warning! Cannot parse file: dino_models/PYRLU_AAO14678_HLP.pdb. Chain number 0.
Warning! Cannot parse file: dino_models/SYMKB_CAE794751_HCC.pdb. Chain number 0.
ERROR! <2 chains for multiple alignment

All .pdb files are in the set directory, and the input list looks like this:

ALEFU_ABO47877_HLP
BREMI_REEF_HLP
CRYCO_Q39474_HCC
KARVE_ABV22220_HLP
LINPO_Q84U55_HLP
PFIPI_ABI14231_HLP
POLGL_CAE8636195_HLP
PROMI_Q6YND9_HLP
PYRLU_AAO14678_HLP
SYMKB_CAE794751_HCC

I've tried with the list having .pdb extensions and without to no avail.

Would you be able to help me out? I'm basing the input list off of the example input list from mTM-align source download.

Thank you

[zcx@umich.edu]

Can you attach the content of "dino_models/" as a zip archive in your next post so that we can check what the issue is?

[zcx@umich.edu]

You issue may be related to https://github.com/pylelab/USalign/issu ... 1356474145 where your pdb file does not have standard atom name. Please check if this is the case.

[hduar008]

Hey everyone,

I tried to see if it was a standard atom name issue, but my example CRYCO seemed to be fine and it's still not being recognized. I've attached the zip file for dino_models/ as requested. Sorry for the inconvenience, and thank you for your help!

[zcx@umich.edu]

I test US-align on your model and do not observe any issue:

Code: Select all

 curl "https://zhanggroup.org/forum/download/file.php?id=60&sid=e7d55819c30ec4ed7cf974e16cdc5b4e" -o dino_models.zip
 unzip dino_models.zip
 USalign -dir dino_models/ dino_models/input_list -suffix .pdb -mm 4

********************************************************************
* US-align (Version 20220924) *
* Universal Structure Alignment of Proteins and Nucleic Acids *
* Reference: C Zhang, M Shine, AM Pyle, Y Zhang. (2022) Nat Methods*
* Please email comments and suggestions to yangzhanglab@umich.edu *
********************************************************************
Average aligned length= 100, RMSD= 1.97, Seq_ID=n_identical/n_aligned= 0.518
Average TM-score= 0.83813 (normalized by length of shorter structure: L=105, d0=3.76)
Average TM-score= 0.79644 (normalized by length of longer structure: L=111, d0=3.89)
Average TM-score= 0.81847 (normalized by average L=108.00 and d0=3.82)
In the following, seqID=n_identical/L.

>ALEFU_ABO47877_HLP.pdb:A L=107 d0=3.80 seqID=0.518 TM-score=0.85391
------------------------------------------------MAPKA-KAKAMK-STAMTKGALADAVATACEMKKKDVIKALASIAEIATAEVKKSGVFTLPGLFRIKSRKKPATKAGKKEI-FGKMCVVKAKPARTIVKAFPVAVLKKEF
>BREMI_REEF_HLP.pdb:A L=116 d0=3.97 seqID=0.457 TM-score=0.78200
----------------MAGAMKAMKTKVMK------------------------AKKVST-AKVMTKGGLTGELANSTELKKADISTILNTLAEIGTKEVKKSGKFVLPGLVMIKTRNKPAKKAGKKVM-FGKEVMVKAQPAKTVVKVFPVSSLKKAI
>CRYCO_Q39474_HCC.pdb:A L=113 d0=3.92 seqID=0.341 TM-score=0.68221
MAPKMKAAMKAMKA-------------------------------------------TAMKGKAMTKTGLAEAWRRRPSFLRRTAGQSWRAWPRSCAAEVKKTGKLTIPGLVMVKTRKKPATKAGKREMF--GKVVLVKASCQDVVKAYPVKALKTDF
>KARVE_ABV22220_HLP.pdb:A L=108 d0=3.82 seqID=0.506 TM-score=0.85011
------------------------------M--LP-PMKS-M--------------KAGA-KKAMTKGALAKALATEHGLKQKACSDVLNSLASIATAEVKKAGIFSIPGLCRIKTRTKPATKAGVRNV-FGKEVKVKAKPARTIVKGYCAAALKKQI
>LINPO_Q84U55_HLP.pdb:A L=104 d0=3.74 seqID=0.554 TM-score=0.87023
---------------------------------------------------MA-PMKAAA-KKAMTKGAIADALATQFELKKTVCGKLINSLAEIATKEVKSSGVFTIPGVCKIKTRTKPATKAGKREI-FGKTVVVKAKPARKVVKAFPVAALKKSI
>PFIPI_ABI14231_HLP.pdb:A L=114 d0=3.94 seqID=0.441 TM-score=0.77751
--------------MA--------------PMKAMKAMKAMK------------A--MKG-GKSITKGGLADAISAETEVKKSDCSKVLTALAEVVAKEVKKTGKVIVPGIARIVTRTKKATKAGKREM-FGKVCIVKAKPARTVVKAFPVAAIKQAV
>POLGL_CAE8636195_HLP.pdb:A L=104 d0=3.74 seqID=0.516 TM-score=0.87511
-------------------------------------------------M-AK-AM-KAA-AKTMTKGALAEALASETGLKKSECNKVVESLAKVATTQVKSAGKFVLPGLCMIKTRQKPATKAGKRMA-FGKEISCKAQPAKTIVKAFCVAALKKSI
>PROMI_Q6YND9_HLP.pdb:A L=102 d0=3.69 seqID=0.510 TM-score=0.87005
----------------------------------------------------MA-PMMK--STVMTKSALTAALAEACEVKRGVIGTALSTLASIATTEAKKNGKFVIPGVVMIKTRQKKATKAGKREI-FGKVVMVKAKPAKTIVKAFPAKALKDEF
>PYRLU_AAO14678_HLP.pdb:A L=103 d0=3.72 seqID=0.506 TM-score=0.79122
-----------------------------------M---APK---------------AMK-GAVMGKAALADALATGCELKRRMSPRSWRVWPRSALGELKKSAVFTLPGICRIKTRRKPATKAGKREV-FGKVVMVKAKPAKTVVKAFPVAALKKQF
>SYMKB_CAE794751_HCC.pdb:A L=113 d0=3.92 seqID=0.450 TM-score=0.82049 *
------------------------------------------MAPAMKSAMKS-KAMKTN-AKAMTKAQLADQLATKSELKKKDVLSVLQNLSEIGANEVTNTGKFVLPGLCMIKTRQKPATKGGTRMM-FGKEVQVKAQKAKTVVKATPLAALKNQI

[sanitaro25]

interesting information