writePDB truncates 4 letters residues to 3 letters

[Cventura18]

Hi,

I am having an issue writePDB with saving 4 letter residues for the probes in druggability simulations. I am using the long_resname feature in parsePDB to select the probes which all have four letter residue name. When I am trying to save the a probe "ACET" for example the corresponding pdb file truncates the residue to ACE in the pdb file.

Best,
Carlos

from prody import *
test = parsePDB('newcgenff.pdb', long_resname = True)
probes = ['IPAM', 'PRO2', 'ACET', 'IBUT', 'ACEM', 'IMIA', 'BENZ']
probe_selstr = 'noh and resname'
prefix = 'dg'
for p in probes:
    sel = test.select('noh and resname ' + p)
    print(p)
    if sel is None:
        continue
                #raise ValueError('probe ' + p + ' is not found in the system')
    hv = sel.getHierView()
    n = hv.numResidues()
    res = next(hv.iterResidues())
    writePDB(prefix + '_' + p + '.pdb', res, warned_long_resname = True)
    plog(str(n) + ' copies of ' + p + ' is found.')
    probe_selstr += ' ' + p
    print(probe_selstr)

REMARK ACET 674
ATOM      1  C1  ACE X 674     -51.279 -38.133  -8.576  0.00  0.00      PROB C
ATOM      2  C2  ACE X 674     -51.282 -36.660  -8.181  0.00  0.00      PROB C
ATOM      3  O1  ACE X 674     -50.157 -36.309  -7.208  0.00  0.00      PROB O
ATOM      4  O2  ACE X 674     -51.105 -35.890  -9.354  0.00  0.00      PROB O
END

[Cventura18]

I believe the code responsible for this is:

if len(resnames[i]) > 3:
                resname = resname[:3]
                if not warned_long_resname:
                    LOGGER.warn('Resname {0} too long, cutting resname to 3 characters as {1}'.format(
                        resnames[i], resname
                    ))
                    warned_long_resname = True

If I change resname[:3] to resname[:4] the corresponding pdb file is now has the residue name ACET instead of ACE.

REMARK ACET 674
ATOM      1  C1  ACET X 674     -51.279 -38.133  -8.576  0.00  0.00      PROB C
ATOM      2  C2  ACET X 674     -51.282 -36.660  -8.181  0.00  0.00      PROB C
ATOM      3  O1  ACET X 674     -50.157 -36.309  -7.208  0.00  0.00      PROB O
ATOM      4  O2  ACET X 674     -51.105 -35.890  -9.354  0.00  0.00      PROB O
END

[jamesmkrieger]

That does break PDB format though, so I think it was decided not to do that on purpose.

What we could do is indeed to limit to 4 characters and remove the space too. We’ll have a look. Thanks

There could be an option to trim it or not