Re: [PyMOL] FW: RE: what is the pymol representation in this figure?

2014-07-11 Thread Sampson, Jared
Hi Yeping - I followed Jared's instruction and then show surface, but the surface is still an incomplete plane, unlike what I wish as in the sample. You will probably have to create new objects for those individual residues to show their surfaces in whole. Otherwise, you only get the portion

[PyMOL] Problem aligning small RNA structures

2014-07-11 Thread Alexis Delabriere
Hello, I want to make a lot of purely structural alignment of pairs of very short RNA structures, from a length varying from 3 to 12 nucleotides (in every alignments both RNA structures will have the same number of nucleotides), which are supposed to have similar geometry. I tried to use ceali

Re: [PyMOL] RE: RE: what is the pymol representation in this figure?

2014-07-11 Thread Gianluca Santoni
You should try, as jared suggested for the surface, to set the color of the sticks only for your selection: set stick_color, color, selection this should't affect the helix, if I'm not wrong. Another way, is to select only the atoms in the sidechain and color only them. Something like color red,

[PyMOL] FW: RE: what is the pymol representation in this figure?

2014-07-11 Thread sunyeping
Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 发件人:孙业平 发送时间:2014年7月11日(星期五) 17:20 收件人:Gianluca Santoni 主 题:RE:[PyMOL] RE: what is the pymol representation in this figure? Dear Gianluca, I followed  Jared's in

Re: [PyMOL] RE: what is the pymol representation in this figure?

2014-07-11 Thread Gianluca Santoni
Dear Yeping, you should check Jared's reponse to your message. I think he gave you all the hints you need. :) Gian On 7/11/14 8:27 AM, sunyeping wrote: > > 发送时间:2014年7月10日(星期四) 21:20 > 收件人:pymol-users > 主 题:Re: [PyMOL] what is the pymol representation in this figure? > > It should be a solid surf