[PyMOL] extra bonds

Hi, In my trajectory movie, there are some minor distortions of some of the residues, but the sticks presentation in pymol seems fine. However, after I loaded the trajectory pdb file use discrete=1, extra bonds would be shown in sticks in those slightly distorted residues. Is there is way to

[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 range

[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 cap

[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 middle

[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 few

[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 transiti

Re: [PyMOL] eMovie question

ame pause at the beginning of the movie and > then edit it out at a later date. > > Simon > > > On 10 May 2009, at 02:01, Jianghai Zhu wrote: > >> Thanks for the suggestion. I have brought the movie back to frame 1 >> before I save the movie or images. So I still

Re: [PyMOL] eMovie question

; menu. Hope this solves your problem. > > Sincerely, > > Carlos > > >>>> Jianghai Zhu 05/08/09 10:51 PM >>> > 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

[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 i

[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 d

Re: [PyMOL] backbone in cartoon

I will make the last question more general. How do I make cartoon go through a specific backbone atom in pymol? Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston

Re: [PyMOL] backbone in cartoon

Another question. After I show C=O as stick, how do I make the cartoon go through the carbonyl carbon? "Side chain helper" can only make sure the cartoon go through the Ca atoms. Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedica

Re: [PyMOL] backbone in cartoon

Hi Tsjerk, Thanks. This works. The sticks didn't show up when I selected oxygen and nitrogen alone. But after I select c+o and n+h, sticks worked very well. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Ha

[PyMOL] backbone in cartoon

t is the best 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 +++

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] ray_trace_mode

adjust 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 +++

[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 Lo

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

Re: [PyMOL] question on cctbx and pymol

Hi, I could not get cctbx work under either MacPymol or PymolX11Hybrid in Mac OS X. Anywhere I can find some instructions to get cctbx work in OS X? Thanks. Jianghai On Aug 23, 2005, at 1:18 PM, Sabuj Pattanayek wrote: Hi, This worked. Thanks, ..Sabuj Robert Campbell wrote: prefixing

[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 worked

[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 1

[PyMOL] macpymol beta bug

, "use most memory in rendering"? Jianghai == Jianghai Zhu Molecular Biology & Biochemistry Purdue University ==

Re: [PyMOL] pymol and Desktop Manager on OS X

No. The game mode doesn't even allow me to switch virtual desktop anymore. Jianghai On Oct 26, 2004, at 12:53 PM, Charles Moad wrote: Have you tried "pymol -G" for game mode? On Tue, 2004-10-26 at 00:33, Jianghai Zhu wrote: Hi, all, Anybody has any experiences of using fu

[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 pymo

[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] Re: PyMOL-APBS os x

I still can't compile it with scott's method. Do you mind share your binary with us? Jianghai == Jianghai Zhu Molecular Biology & Biochemistry Purdue University == On Jul 15, 2004, at 7:47 PM, William Scott wrote: The best way to ov

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

using 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

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

Re: [PyMOL] protein surface

gt; of the water atoms when in contact with the protein. > > PyMOL can only show solvent accessible surfaces using the dot > or sphere representations: > > for dots: > > show dots > set dot_mode,1 > set dot_density,3 > > for spheres: > > alter all,vdw=vdw+1.

[PyMOL] protein surface

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

[PyMOL] CA only pdb file

header. Thanks. Jianghai -- === Jianghai Zhu Biochemistry & Molecular Biology Purdue University Tel: 765-4949249 (O) 765-466 (H) ===

[PyMOL] how to use util.rainbow?

Hi, all, I was trying to use a command to do rainbow coloring. After I entered util.rainbow, pymol(0.86) hung up there. I could not find any document or help on how to use util.rainbow. Could someone give me some suggestions? Thanks. Jianghai -- === Jianghai Zhu