From: Michael W. <we...@st...> - 2006-06-30 06:22:36
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Hi, I have a question concerning the "spheres" representation. According to my rough estimation the spheres drawn for individual atoms/ions don't seem not match experimental atomic/ionic radii if I compare different elements. Is that correct (I quickly checked for oxygen, phosphorus and magnesium2+)? Furthermore, is it possible to manually assign radii to selected atoms? Best regards, Michael. |
From: Tsjerk W. <ts...@gm...> - 2006-06-30 08:35:15
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Hi Michael, The answer to the second question is: yes alter selection,vdw=1.0 will change the radius of selected atoms to 1.0 angstrom. Cheers, Tsjerk On 6/30/06, Michael Weber <we...@st...> wrote: > Hi, > I have a question concerning the "spheres" representation. According to my > rough estimation the spheres drawn for individual atoms/ions don't seem not > match experimental atomic/ionic radii if I compare different elements. Is > that correct (I quickly checked for oxygen, phosphorus and magnesium2+)? > Furthermore, is it possible to manually assign radii to selected atoms? > > Best regards, > Michael. > > > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 |
From: <gre...@un...> - 2006-07-01 11:33:22
Attachments:
mol.png
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Dear Michael, I do not agree with you; I never observed any variation between sphere representation and experimental data. But to test the accuracy of the sphere size, I did the following = sequence: 1) I created a molecule composed of one hydrogen and one oxygen, with a "fake" distance of 1.52 A between the two atoms. Here is the MOL file corresponding to this molecule (you might save it using any text editor, = the first line should be the '962', and save it with the .mol extension). 962 molecule 2D 2 1 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5200 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 M END 2) I opened this molecule in PyMOL, and displayed it with line representation. 3) I created a new object from the O only, displayed as sphere (with a transparency of 0.5). 4) Ray-tracing... gives the image attached to this e-mail. One can see that the O-H line, having a length of 1.52A, corresponds = EXACTLY to the sphere of the oxygen.=20 I checked using the same procedure the sphere size of Mg and here I also obtained a perfect match between a bond length of 1.73A and the sphere. = So I don't understand how you came to the conclusion that there is a mismatch between PyMOL values and experimental values. Best regards, Greg -----Original Message----- From: Michael Weber [mailto:we...@st...]=20 Sent: vendredi, 30. juin 2006 08:23 To: pym...@li... Subject: [PyMOL] spheres representation and atomic / ionic radii Hi, I have a question concerning the "spheres" representation. According to = my=20 rough estimation the spheres drawn for individual atoms/ions don't seem = not=20 match experimental atomic/ionic radii if I compare different elements. = Is=20 that correct (I quickly checked for oxygen, phosphorus and magnesium2+)? = Furthermore, is it possible to manually assign radii to selected atoms? Best regards, Michael.=20 |