From: Anasuya D. <an...@mb...> - 2012-07-23 07:16:45
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Hi Pymol-users, I need to select only the atoms [and NOT complete amino acid residues] which are lying in a radius of 4.5 Angstroms from the ligand from a ligand-bound protein structure. I am aware that the command: select site, br. resn FAD and chain A and resi 45 around 4.5 and not HET selects complete amino acid residues which are lying in the vicinity of the ligand within a radius of 4.5 Angstroms. However, I am only interested in selecting all the atoms which are present in this region and "not the complete amino acid residues." How can this be done? Please let me know. - Anasuya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. |
From: Thomas H. <sp...@us...> - 2012-07-23 08:04:52
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Hi Anasuya, "br." is short for "byres" (by residue). So just drop that from your selection expression. select site, (resn FAD and chain A and resi 45) around 4.5 and not HET Cheers, Thomas Anasuya Dighe wrote, On 07/23/12 09:00: > Hi Pymol-users, > > I need to select only the atoms [and NOT complete amino acid residues] which are > lying in a radius of 4.5 Angstroms from the ligand from a ligand-bound protein > structure. > I am aware that the command: select site, br. resn FAD and chain A and resi 45 > around 4.5 and not HET selects complete amino acid residues which are lying > in the vicinity of the ligand within a radius of 4.5 Angstroms. > However, I am only interested in selecting all the atoms which are present in > this region and "not the complete amino acid residues." > How can this be done? > Please let me know. > > - Anasuya -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |