Re: [Jmol-users] select WITHIN(...)

On 5/24/2013 10:49 AM, Robert Hanson wrote: On Fri, May 24, 2013 at 9:54 AM, Angel Herráez > wrote: Hello Pshemak > Finally, can the selected groups of atom (ions) be given a name (ID) so > they could be referred to without repeating the selectio

Re: [Jmol-users] select WITHIN(...)

On Fri, May 24, 2013 at 9:54 AM, Angel Herráez wrote: > Hello Pshemak > > > Finally, can the selected groups of atom (ions) be given a name (ID) so > > they could be referred to without repeating the selection criteria? > > Yes, two ways: using the "define" command or using a JmolScript variable

Re: [Jmol-users] select WITHIN(...)

Hello Pshemak > Consider NaCl crystal structure. I have a specific Na+ in mind. Let's > say @6. Now, I want to select all chlorides that are within 6 A of that > specific Na+. How could I do that? select _Cl and within(6.0, atomNo=6); select _Cl & within(6.0, @6); //same but shorter you migh

[Jmol-users] select WITHIN(...)

I have question about the syntax of the "select within). Perhaps best illustrated on an example. Consider NaCl crystal structure. I have a specific Na+ in mind. Let's say @6. Now, I want to select all chlorides that are within 6 A of that specific Na+. How could I do that? If I want to do t

Re: [Jmol-users] select within( radius, ... ) in large pdb files

Alex - Ursprüngliche Mail - > Von: "Robert Hanson" > An: jmol-users@lists.sourceforge.net > Gesendet: Montag, 6. Dezember 2010 20:24:35 > Betreff: Re: [Jmol-users] select within( radius, ... ) in large pdb files > Looks to me like you are using the wrong notation there. You wan

Re: [Jmol-users] select within( radius, ... ) in large pdb files

Looks to me like you are using the wrong notation there. You want: select within(5.0, 113 and protein) select within(5.0, atomno=1795) -- no braces -- specify protein -- "5.0, not 5,0" -- US notation there on numbers, not EU -- not "select within(5, 0, 113)" I think what that does is to say w

[Jmol-users] select within( radius, ... ) in large pdb files

Hi, I think there is some bug in the WITHIN(distance, withinAllModels, atomExpression) function. It selects more then it is supposed to: http://proteinformatics.charite.de/jmol-test/html/select_within.html the page shows two examples where you can select for each first the atomExpression aroun

Re: [Jmol-users] select within(BASEPAIR woes

Oh, I see what you mean. Yes, I agree that needs to be clearly mentioned. 2010/5/21 Angel Herráez > > I don't think so. There may have been CG in RasMol, but there was > > never any capability that I know of in Jmol to detect hydrogen-bonded > > base pairs like that. > > Well, certainly no detec

Re: [Jmol-users] select within(BASEPAIR woes

> I don't think so. There may have been CG in RasMol, but there was > never any capability that I know of in Jmol to detect hydrogen-bonded > base pairs like that. Well, certainly no detection of base pairs. That's why I think the distinction must be made clear. The sets are indeed defined in

Re: [Jmol-users] select within(BASEPAIR woes

fixed -- will upload shortly. Simple logic error. On Fri, May 21, 2010 at 8:37 AM, Robert Hanson wrote: > > > 2010/5/21 Angel Herráez > > I am seeing this as a nice, recent addition in the "new.htm" >> document: >> >> 122. select within(BASEPAIR) >> # Jmol 12.0.RC5 adds the capability to select

Re: [Jmol-users] select within(BASEPAIR woes

2010/5/21 Angel Herráez > I am seeing this as a nice, recent addition in the "new.htm" > document: > > 122. select within(BASEPAIR) > # Jmol 12.0.RC5 adds the capability to select atoms based on RNA or > DNA base pairing. Thank you, Neena Grover! load 2qnh.pdb.gz;zoom > 300;wireframe -0.4;display

[Jmol-users] select within(BASEPAIR woes

I am seeing this as a nice, recent addition in the "new.htm" document: 122. select within(BASEPAIR) # Jmol 12.0.RC5 adds the capability to select atoms based on RNA or DNA base pairing. Thank you, Neena Grover! load 2qnh.pdb.gz;zoom 300;wireframe -0.4;display rna;select *.P;label %n%r;select rn

Re: [Jmol-users] SELECT WITHIN

But that is a bug -- now fixed. On Sat, Jan 2, 2010 at 2:45 PM, Stephen Hillier wrote: > Figured it out thanks, > > hkl should be in quotation marks > > e.g. > > select within(3.0, "hkl", {0 0 1}) > > steve > > > > > > >>> "Stephen Hillier" 01-Jan-10 10:05 PM >>> > I also have question about se

Re: [Jmol-users] SELECT WITHIN

try putting the hkl in quotation marks: select within(3.0, "hkl", {0 0 1}) On Fri, Jan 1, 2010 at 4:05 PM, Stephen Hillier wrote: > I also have question about selecting > > after loading a range of unit cells from a CIF file I'm trying to figure > out how to use 'select within..' to select som

Re: [Jmol-users] SELECT WITHIN

Figured it out thanks, hkl should be in quotation marks e.g. select within(3.0, "hkl", {0 0 1}) steve >>> "Stephen Hillier" 01-Jan-10 10:05 PM >>> I also have question about selecting after loading a range of unit cells from a CIF file I'm trying to figure out how to use 'select

[Jmol-users] SELECT WITHIN

I also have question about selecting after loading a range of unit cells from a CIF file I'm trying to figure out how to use 'select within..' to select some atoms near a plane e.g: but I get an error message and can't figure out what I'm doing wrong: $ load "" {3 3 1} packed $ select within(3