If you happen to be a user of VMD, then unless I've forgotten something or made a typo the below script should do the trick. Just feed it a list of PDB IDs in pdblist.txt and a list of residue names in reslist.txt (one entry per line in each case), and it should spit out a comma-delimited text file listing the heavy-atom count for each lipid residue present. It would double-count atoms in residues with altlocs, but otherwise should behave fine.
proc count_lipid_atoms {} {
set in [open pdblist.txt r]
set pdbs [split [read $in] "\n"]
close $in
set in [open reslist.txt r]
set resnames [split [read $in] "\n"]
close $in
set out [open lipid_summary.txt w]
puts $out "PDB ID,Name,Chain,Resid,Atom Count"
foreach pdbentry $pdbs {
if {catch {mol new $pdbentry} } {continue}
set lipids [atomselect top "resname $resnames"]
set lipid_res_list [lsort -unique [$lipids get residue]]
$lipids delete
foreach lipid $lipid_res_list {
set thislipid [atomselect top "residue $lipid and noh"]
set thislipidname [lsort -unique [$thislipid get resname]]
set thislipidchain [lsort -unique [$thislipid get chain]]
set thislipidresid [lsort -unique [$thislipid get resid]]
set thisatomcount [llength [$thislipid get index]]
puts $out "$pdbentry,$thislipidname,$thislipidchain,$thislipidresid,$thisatomcount"
$thislipid delete
}
mol delete top
}
close $out
}
________________________________________
From: Michael Wiener <[log in to unmask]>
Sent: Tuesday, 2 February 2016 6:26 AM
To: Tristan Croll
Cc: [log in to unmask]
Subject: Re: [ccp4bb] Lipid structures in experimentally-determined pdb depositions?
Nice idea. Thanks. Lipid nomenclature has not always been as
standardized as one would like, particularly for fragments, but, agreed,
a well-crafted query is a fine way to go.
-MW
On 2/1/16 3:21 PM, Tristan Croll wrote:
> If you have a list of residue names you're interested in, that's a quite straightforward analysis to script. The PDB website can be used to generate a list of structures containing the residue(s) of interest, then it's just a few lines of code to download them in turn and count atoms.
>
>
>
> Tristan Croll
> Lecturer
> Faculty of Health
> School of Biomedical Sciences
> Institute of Health and Biomedical Engineering
> Queensland University of Technology
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> Kelvin Grove QLD 4059 Australia
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>
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>
>
>> On 1 Feb 2016, at 9:08 PM, Michael Wiener <[log in to unmask]> wrote:
>>
>> Colleagues,
>>
>> I have a query for which you may be able to assist:
>>
>> How many PDBs, obtained from experiment (i.e., x-ray, NMR, cryo-EM, and not MD), exist for largely intact lipid molecules bound to proteins? There are quite a few with fragments of lipid molecules (such as the lipid tails), but I'm interested in structures of nearly-to-fully complete lipid molecules. And, these structures need not be of integral membrane proteins.
>>
>> I wrote a book chapter related to this ~ a decade ago (http://onlinelibrary.wiley.com/doi/10.1002/3527606769.ch5/summary) for membrane proteins, but much has changed since then. Any assistance would be greatly appreciated.
>>
>> Thank you.
>>
>> -MW
>>
>> --
>> Michael C. Wiener, Ph.D., Professor
>> Department of Molecular Physiology and Biological Physics
>> University of Virginia
>> PO Box 800886
>> Charlottesville, VA 22908-0886
>> 434-243-2731 (office)
>> 434-243-2730 (lab)
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