## [PyMOL] Get number of residues in model

 [PyMOL] Get number of residues in model From: Martin Hediger - 2011-11-29 14:50:32 ```Dear List How can I compute the numbers of residues in a model? Martin ```

 [PyMOL] rotate translate two different objects indpendently and legend From: Christian Roth - 2011-11-28 16:31:22 ```Dear all, I have a two chain protein and I want translat and rotate it using the commands translate and rotate. It is complicate to choose the rigth angel, because I cannot see the rotation axis. Is there a way to draw the axis system for the objects to see around which axis and how much I must rotate every single object. Does every object have is own axis system or is there a common system for all objects? When I color my protein according to the B-values is it possible to include a kind of a legend like for the elctrostatics when I use APBS to get an idea about the minimum and maximum value? Thanks in advance and Best Regards Christian ```
 Re: [PyMOL] rotate translate two different objects indpendently and legend From: Jason Vertrees - 2011-11-28 18:39:13 ```Hi Christian, > I have a two chain protein and I want translat and rotate it using the > commands translate and rotate. It is complicate to choose the rigth angel, > because I cannot see the rotation axis. Is there a way to draw the axis system > for the objects to see around which axis and how much I must rotate every > single object. Does every object have is own axis system or is there a common > system for all objects? See http://www.pymolwiki.org/index.php/Axes. Each object has its own transformation matrix. Rotate and translate can act upon that matrix. See http://www.pymolwiki.org/index.php/Get_object_matrix. > When I color my protein according to the B-values is it possible to include a > kind of  a legend like for the elctrostatics when I use APBS to get an idea > about the minimum and maximum value? An easy way is the following, but has two problems: (1) you're not ensured the correct 1-1 mapping; (2) when you adjust the ramp the lines colors don't change. But, it does work: # fetch an example protein fetch 1foo, async=0 # color it by b-factor spectrum b, rainbow # get the list of b-factors x = [] cmd.iterate("1foo", "x.append(b)", space={'x':x}) # create the ramp across the range cmd.ramp_new("myRamp", "1foo", [min(x), max(x)], "rainbow") If I can recall the other way of mapping the ramp color to the lines, I'll let you know. Right now it escapes me. Cheers, -- Jason > Thanks in advance and Best Regards > > Christian > > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jason.Vertrees@... (o) +1 (603) 374-7120 ```
 [PyMOL] Get number of residues in model From: Martin Hediger - 2011-11-29 14:50:32 ```Dear List How can I compute the numbers of residues in a model? Martin ```
 Re: [PyMOL] Get number of residues in model From: Jason Vertrees - 2011-11-29 15:27:02 ```Hi Martin, You get three options: (1) You can count alpha carbons: fetch 1rx1, async=0 count_atoms n. CA (2) But, a protein could be missing alpha carbons then this is more complete (and the technique worth noting): n=0 select qq, polymer select pp, None python while cmd.count_atoms("qq"): cmd.select("pp", "br. first qq") cmd.select("qq", "qq and not pp") n+=1 python end print "count_atoms: %d" % n If you put: select qq, * you'll get a higher count (160) because one atom in 1rx1's inorganic set is also named "CA". (3) The shorter version of (2) is: print len(cmd.get_model("poly").get_residues()) Cheers, -- Jason On Tue, Nov 29, 2011 at 9:50 AM, Martin Hediger wrote: > Dear List > How can I compute the numbers of residues in a model? > > Martin > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jason.Vertrees@... (o) +1 (603) 374-7120 ```
 Re: [PyMOL] Get number of residues in model From: Tsjerk Wassenaar - 2011-11-29 16:00:50 ```Hi Martin, Here's a fourth option (and the technique worth noting :p ): print len( set( [(i.chain,i.resi,i.resn) for i in cmd.get_model(selection).atom] ) ) Cheers, Tsjerk On Tue, Nov 29, 2011 at 4:26 PM, Jason Vertrees wrote: > Hi Martin, > > You get three options: > > (1) You can count alpha carbons: > > fetch 1rx1, async=0 > > count_atoms n. CA > > > (2) But, a protein could be missing alpha carbons then this is more > complete (and the technique worth noting): > > n=0 > select qq, polymer > select pp, None > python > while cmd.count_atoms("qq"): >  cmd.select("pp", "br. first qq") >  cmd.select("qq", "qq and not pp") >  n+=1 > python end > print "count_atoms: %d" % n > > If you put: > > select qq, * > > you'll get a higher count (160) because one atom in 1rx1's inorganic > set is also named "CA". > > > (3) The shorter version of (2) is: > > print len(cmd.get_model("poly").get_residues()) > > Cheers, > > -- Jason > > > On Tue, Nov 29, 2011 at 9:50 AM, Martin Hediger wrote: >> Dear List >> How can I compute the numbers of residues in a model? >> >> Martin >> >> ------------------------------------------------------------------------------ >> All the data continuously generated in your IT infrastructure >> contains a definitive record of customers, application performance, >> security threats, fraudulent activity, and more. Splunk takes this >> data and makes sense of it. IT sense. And common sense. >> http://p.sf.net/sfu/splunk-novd2d >> _______________________________________________ >> PyMOL-users mailing list (PyMOL-users@...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@... >> > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jason.Vertrees@... > (o) +1 (603) 374-7120 > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@... > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ```