Bugs item #916570, was opened at 2004-03-15 12:51 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=916570&group_id=23629
Category: Scripting Group: None Status: Open Resolution: None Priority: 5 Submitted By: Michael T Howard (michaelthoward) Assigned to: Michael T Howard (michaelthoward) 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 ---------------------------------------------------------------------- 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: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
