Hi,
I am running into an issue with MM-align. I have two monomers that I want to superposed, saved in PDB format, attached. For a reason I don't understand, MM-align tries to align two chains of model01.pdb. I can see that the sequence is duplicated in UPPER case, with a space in between. However model01 only has one chain, as it is a monomer.
Steps to reproduce:
./MMalign model01.pdb model02.pdb
Generates the following output:
**************************************************************************
* MM-align *
* Aligning protein complex structure by Dynamic Programming *
* Comments on the program, please email to: zhng@umich.edu *
**************************************************************************
Protein 1:model01.pd Size= 261
Protein 2:model02.pd Size= 258 (TM-score is normalized by 258)
Aligned length= 257, RMSD= 1.57, TM-score=0.94660, ID=0.996
-------- rotation matrix to rotate Chain-1 to Chain-2 ------
i t(i) u(i,1) u(i,2) u(i,3)
1 32.9895352759 -0.1835116774 0.2813259282 -0.9419018985
2 25.2317022225 -0.1682269668 0.9350513192 0.3120556330
3 12.4437071360 0.9685159534 0.2157191520 -0.1242662284
(":" denotes the residue pairs of distance < 5.0 Angstrom)
ppyslfeawakpvqpfaiwpgvwyvgtenlssvllttpqghilidagldasapqirrniealgfrmadiryiansharldqaggiarlkawsgarviashanaeqmarggkedfalgdalpfppvtvdmeaqdgqqwhlggvtlaaiftpghlpgatswkvtladgktliyadslatpgyplinnrnyptlvedirrsfarleaqqvdiflankgerfglmdkmarkargennafidkaglaryvaqsraafekqlaaqra- PPYSLFEAWAKPVQPFAIWPGVWYVGTENLSSVLLTTPQGHILIDAGLDASAPQIRRNIEALGFRMADIRYIANSHARLDQAGGIARLKAWSGARVIASHANAEQMARGGKEDFALGDALPFPPVTVDMEAQDGQQWHLGGVTLAAIFTPGHLPGATSWKVTLADGKTLIYADSLATPGYPLINNRNYPTLVEDIRRSFARLEAQQVDIFLANKGERFGLMDKMARKARGENNAFIDKAGLARYVAQSRAAFEKQLAAQRA
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.
-----feawakpvqpfaiwpgvwyvgtenlssvllttpqghilidagldasapqirrniealgfrmadiryiansharldqaggiarlkawsgarviashanaeqmarggkedfalgdalpfppvtvdmeaqdgqqwhlggvtlaaiftpghlpgatswkvtladgktliyadslatpgyplinnrnyptlvedirrsfarleaqqvdiflankgerfglmdkmarkargennafidkaglaryvaqsraafekqlaaqraqp----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
(Odd no chains of both proteins are in lower case and Even no chains of both proteins are in UPPER case)
I would have expected the output to echo the chain only once, something like this, instead:
ppyslfeawakpvqpfaiwpgvwyvgtenlssvllttpqghilidagldasapqirrniealgfrmadiryiansharldqaggiarlkawsgarviashanaeqmarggkedfalgdalpfppvtvdmeaqdgqqwhlggvtlaaiftpghlpgatswkvtladgktliyadslatpgyplinnrnyptlvedirrsfarleaqqvdiflankgerfglmdkmarkargennafidkaglaryvaqsraafekqlaaqra-
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.
-----feawakpvqpfaiwpgvwyvgtenlssvllttpqghilidagldasapqirrniealgfrmadiryiansharldqaggiarlkawsgarviashanaeqmarggkedfalgdalpfppvtvdmeaqdgqqwhlggvtlaaiftpghlpgatswkvtladgktliyadslatpgyplinnrnyptlvedirrsfarleaqqvdiflankgerfglmdkmarkargennafidkaglaryvaqsraafekqlaaqraqp
I am running the latest MMalign.f from https://zhanglab.ccmb.med.umich.edu/MM-align/ , last update in 2013, and freshly compiled with gfortran as instructed on the page linked.
Is there something wrong with my file or am I hitting a bug in MM-align?
Thanks,
Xavier