Dear Modellers, As per the ongoing discussions between thomas gaillard and Ben Webb, the two cases i.e. employing HETATM MSE as MET in template(s) leads to a model different than the case, when they are taken as HETATM only. Surprisingly, MODERLLER consideration is wrong in 1 case, as i realized. One template for a CASP9 target was an enzyme. So its structural mutual orientation of domains was more accurate when MSE was considered as compared to the case, when such HETATM MSE records were forced as MET. Therefore, while modelling a target and also knowing the available hetatom environment, consideration of MSE record makes sense. Whereas on the other hand, modelling an unknown target, the MODELLER's forceful mapping of MSE to MET is acceptable. In the former case, CG-SD-CE bond length, angle and topology is disturbed when it is considered as MET. Therefore, the distance map based model accuracy was found higher in first case and the same as inferior in the latter case. Therefore, I believe the best solution should be to put an option in Model-multiple or any such modelling script as env_io_hetatm_default_statement=True if such HETATM records need to be considered as standard amino acids or, env_io_hetatm_default_statement=False, if such HETATM records need to be considered as such with no alteration of their bond lengths, angles and inter-atomic orientation/switchings.

This would help us to improve the accuracy of model's Hydrogen bonding network for sure.

Regards, Ashish

Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

Message: 1 Date: Mon, 25 Jun 2012 15:41:56 -0700 From: Modeller Caretaker modeller-care@salilab.org To: Thomas Gaillard thomas.gaillard@polytechnique.edu Cc: modeller_usage@salilab.org Subject: Re: [modeller_usage] HETATM MSE records Message-ID: 4FE8E934.7020909@salilab.org Content-Type: text/plain; charset=UTF-8; format=flowed

On 6/25/12 10:33 AM, Thomas Gaillard wrote: > I have noticed that some HETATM records are read by Modeller and > automatically handled as corresponding standard residues (for example > MSE -> MET)

Actually MSE -> MET is the only such translation done.

> I would like to know if you could suggest a way to disable this > behaviour and really ignore all HETATM records.

Unfortunately there isn't any way to do that - it is hardcoded into the PDB reader. Why do you want to treat MSE as HETATMs anyway? There may be a better way to achieve your goal.

Ben Webb, Modeller Caretaker