Bugs item #916570, was opened at 2004-03-15 12:51 Message generated for change (Settings changed) made by migueljmol You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=916570&group_id=23629
Category: Scripting Group: None Status: Closed Resolution: Fixed Priority: 5 Submitted By: Miguel (michaelthoward) >Assigned to: Miguel (migueljmol) Summary: occupancy as an atom property Initial Comment: -------- Original Message -------- Subject: Request for 'select occupancy [operator] [value]' in Jmol From: "Miguel Howard" <[EMAIL PROTECTED]> Date: Mon, March 15, 2004 12:49 To: <[EMAIL PROTECTED]>, <[EMAIL PROTECTED]>, <[EMAIL PROTECTED]> > what we need is a new select command to be implemented in Jmol: > > select occupancy [value] > select occupancy < [value] > select occupancy > [value] I assume that this first example is supposed to have some comparision operatoer ... one of: > >= == <= < != (or their syntatical equivalents) > This should be relatively easy to implement, since it is identical to > the existing "select temperature [operator] [value]" command, Yes, adding 'occupancy' as an atom property that can be used in atom expressions can be easily done. > just changing the field in the PDB ATOM record that is used. (See > http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html) > > "select temperature" is not well documented in the RasMol manual! The > above "comparisons" section is the only place I found it. We will also add an operator to the label formatter so that this data can be output. label %o neither '%o' nor '%O' are used yet. Q: Do you want to use lowercase 'o' or uppercase 'O' ? (we would use the lowercase version unless we want to reserve it for some other atom property that is more popular) I opened up a few .pdb files and took a look. The only values I saw were '0.00' or '1.00' Q: Is this a 'binary' field, with values of 0.00 and 1.00 only? Q: If so, why did the .pdb make it a float? Q: If not, what is the range of possible value? Q: If I see a file that has spaces in this field, is the default value 1 ? Finally ... Christopher wrote: >> It is not uncommon for PDB files to >> contain atoms with zero occupancy. Therefore, they really aren't >> part >> of the model. I forget this fact all the time when looking at >> models. >> Many people don't even realize this. Eric wrote: > "Occupancy" is the term used for the PDB format > (http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html) Q: Can someone give me a 25 word description of what occupancy means? Thanks, Miguel ---------------------------------------------------------------------- Comment By: Miguel (michaelthoward) Date: 2004-03-19 00:28 Message: Logged In: YES user_id=608250 This has been implemented as an integer value in the range 0-100 Undefined values (including models from non-pdb files) are given the value 100. %q can be used within the label field This will be released in 10pre7 ---------------------------------------------------------------------- Comment By: Eric Martz (emartz) Date: 2004-03-18 23:16 Message: Logged In: YES user_id=916154 1. Yes, "select occupancy [operator] [value]" should always have an operator. I was in error when I implied that the absence of an operator was synonymous with equality. 2. Although most PDB files have all occupancies set to 1.00, some have 0.00 values, and some have other values. It is not a binary field. 3. Please see http://molvis.sdsc.edu/protexpl/igloss.htm#temperature for a very short introduction to "occupancy" and "temperature". ---------------------------------------------------------------------- Comment By: Miguel (michaelthoward) Date: 2004-03-17 13:45 Message: Logged In: YES user_id=608250 -------- Original Message -------- Subject: RE: Request for 'select occupancy [operator] [value]' in Jmol From: "Miguel Howard" <[EMAIL PROTECTED]> Date: Wed, March 17, 2004 13:45 To: <[EMAIL PROTECTED]> Christopher wrote: >>Q: Do you want to use lowercase 'o' or uppercase 'O' ? (we would use >> the lowercase version unless we want to reserve it for some other >> atom property that is more popular) > > The abbreviations I've seen (and used) for occupancy are "Q" (or "q"), > or less commonly "Occ". For example, the programs CNS, XPLOR, and > PyMol use upper and lower case "Q" for occupancy. We will use lower case 'q' ... as in PyMol >>Q: If not, what is the range of possible value? >>Q: If I see a file that has spaces in this field, is the default value >> 1 ? > > Its value can range from 0.00 to 1.00, but the default value would be > 1.00. Good > I would also note that multiple conformations or partial occupancies > can > apply to ANY atom in a PDB file: ligands, solvent, backbone or side > chain. Often solvent atoms modeled at partial occupancies don't have > "alternate conformations". Jmol currently only chooses the first confirmation when multiple confirmations are present. > The density is simply too poor or too weak > to warrant saying that the solvent atoms are always present at that > particular position in the unit cell. I am not a chemist ... that was helpful ... thanks. > Thanks, > Christopher Bottoms > University of Missouri-Columbia I hope to implement this within the next few weeks. Miguel ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=916570&group_id=23629 ------------------------------------------------------- This SF.Net email is sponsored by: Oracle 10g Get certified on the hottest thing ever to hit the market... Oracle 10g. 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