[PyMOL] SS in a trajectory

Hi, I have a trajectory file, in which two short helices would merge into one long helix. However, when I play the trajectory in Pymol as cartoon, the long helix would still be shown as two helices with a loop in between. Is there a way to force Pymol to show a long helix for a specific

[PyMOL] Quicktime movie saving

Hi, In MacPymol, I can save a movie as a quicktime movie by File-Save Movie As-Quicktime…. What is the equivalent command for this function? Thanks. --Jianghai -- Precog is a next-generation analytics platform

[PyMOL] movie for morphing

Hi, I have a pdb containing the morphing. I can play the movie with the loaded pdb file. Now I want to start the movie with rocking the first state for a few seconds and end the movie with rocking the last state for a few seconds. How do I do that? Can I rock or nutate a state in the

[PyMOL] movie for morphing

Hi, I have a pdb containing the morphing. I can play the movie with the loaded pdb file. Now I want to start the movie with rocking the first state for a few seconds and end the movie with rocking the last state for a few seconds. How do I do that? Can I rock a state in the middle for a

[PyMOL] refinement in morph

Hi, If I turn on the refinement option in morph, the non-covalently bonded atoms like metals and waters are moving around a lot. However, if I turn off the refinement, there are some distortions in my protein. Is there a way to make the non-covalently bonded atoms just move along the

[PyMOL] eMovie question

Hi all, I am trying to make a simple movie using eMovie. I rotate the molecule 360 degrees and then move to another region. The movie is fine when I play it in pymol. However, when I tried to save the movie as sequential images or as a movie, the movie won't play until 70ish frames and

[PyMOL] question about SUPER

structures cannot be aligned anymore even though the first few structures are aligned quite well. So is this a bug? Jianghai Jianghai Zhu, PhD Immune Disease Institute Dept. of Pathology Harvard Medical School 200 Longwood Ave. Boston, MA 02115 Tel: 617-278-3211 Fax: 617-278-3232

[PyMOL] color key using ConSurf

Hi all, I am using ConSurf server to calculate the consurf scores and trying to generate pictures in Pymol. I followed their instructions and everything worked fine. I just have one question. Does anyone know how to generate the color key in Pymol? The color key image on the website

[PyMOL] backbone in cartoon

way to show the backbone nitrogen? Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++

[PyMOL] ray_trace_mode

the thickness of the black outline in the ray-traced image? Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++

Re: [PyMOL] ray_trace_mode

Yes, this strategy works very well. Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232

[PyMOL] hydrogen bonds displaying

Hi all, How can I display hydrogen bonds of one protein in pymol just like the Roving Detail in Demonstration? Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston

Re: [PyMOL] Mac Flicker Issue Workaround

USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: Jianghai Zhu [mailto:z...@purdue.edu] Sent: Saturday, November 05, 2005 7:49 PM To: Warren DeLano Subject: Re: [PyMOL] Mac Flicker Issue Workaround I

[PyMOL] background color

Hi, all, I am trying to change the color of the background in pymol. I know I can change the background color from menu to white, black, light grey and grey. But I want some other color. set bg_rgb, [51,153,153] or set_color newcolor=[51,153,153] bg_color newcolor but none of them

[PyMOL] transparency surface

Hi, all, I have several objects using surface presentation. Is there a way to make the surface of one object to be transparent and the the surfaces of other objects still solid? Thanks. Jianghai

[PyMOL] perspective rendering

Hi, all, I am trying to render my picture in a perspective view in pymol 0.98. Is there a way to make the perspective effect more dramatic than the default way? I mean to make the far end smaller and the close end bigger. Thanks. Jianghai

[PyMOL] density around ligand

Hi, all, Is there a way in Pymol to draw electron density only around my ligand? Thanks. Jianghai

[PyMOL] question about side chain helper

Hi, all I am trying to make a picture in pymol. I have my protein in cartoon presentation and some residues in stick presentation. When I turn on side chain helper, it works beautifully except that my glycines disappeared. Is there any way to get the glycines back? Thanks. Jianghai

[PyMOL] a minor bug in MacPymol 0.98 beta 27

Hi, I found out that once in a while macpymol lost memories of previous commands. so the up key could not bring the previous commands back in the external window. I don't know if this only happened to me. It could be a minor bug. Jianghai

Re: [PyMOL] macpymol beta bug

Thanks. The new beta is very good. Especially like the side_chain_helper. Now I just wonder how I can get APBS plugin work under MacPymol. Jianghai == Jianghai Zhu Molecular Biology Biochemistry Purdue University == On Dec 4, 2004, at 12:55 PM

[PyMOL] macpymol beta bug

== Jianghai Zhu Molecular Biology Biochemistry Purdue University ==

[PyMOL] pymol and Desktop Manager on OS X

Hi, all, Anybody has any experiences of using full-screen pymol and desktop manager at the same time on OS X? When I am running desktop manager and put pymol into full screen mode, I found every virtual desktop is full-screen pymol. I like to use this to switch back and forth between my

[PyMOL] unit cell

Hi, folks, In pymol, how do you draw a unit cell? The cell constants are in the pdb file and the manual says pymol can display unit cell. I just could not figure out how to do it. Thanks. Jianghai == Jianghai Zhu Molecular Biology Biochemistry Purdue University ==

Re: [PyMOL] A couple of quick PyMOL + APBS notes

fink g77, that will be great. Jianghai == Jianghai Zhu Molecular Biology Biochemistry Purdue University == On Jul 15, 2004, at 6:52 PM, Douglas Kojetin wrote: (this might be better suited on an APBS list, but i figured i'd give it a shot here) I

Re: [PyMOL] Powermate dial with Pymol on OS X

This works, but it could ruin my sessions which are very important for us. Warren, is it possible to add the support of powermate into PyMol or MacPyMol? Since it works perfectly with O, I think it could be a very helpful control tool for PyMol too. == Jianghai Zhu

[PyMOL] color choices

Hi, all, When I use color command, how many choices do I have for colors? Can I use direct rgb value? Thanks. Jianghai -- Jianghai Zhu Biochemistry Molecular Biology Purdue University Tel: (765)494-9247

[PyMOL] protein surface

? like msms format, grasp format, etc. Thanks. Jianghai -- === Jianghai Zhu Biochemistry Molecular Biology Purdue University Tel: 765-4949249 (O) 765-466 (H) ===