[PyMOL] cut protein in half
Dear pymol users, I want to make a cross-section on a ion tunnel protein to cut it in half and observe the intenal characters of the tunnel. According to materials on web, I runed the following commands: hide all show surface set ray_trace_mode, 0 set two_sided_lighting, off set ray_interior_color, grey50 But I didn't see any obvious change on the structure except that the protein became dim. Could you help me with that? Tnanks in advance! Yeping Sun-- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] get coordinate
Dear pymol users, Could anyone tell me how to show the coordinate of a selected atom? Regards, Yeping Sun -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] caver plugin
Dear pymol users, Does anyone use the caver plugin of pymol to analyze a ion channel? I don't know how to specify selection for the starting of plugin. Should the starting point be at the center of the channel where there is empty and no atoms in the molecule? or should it be certain atom of the molecule? If it should be the latter, what is the correct syntax of the selection? For example, if I want to select CA atom of Try21 in chain A, should I input the following command? chain A and resid 21 and CA But this is wrong and does not work. Could someone give me some tutorial? Thanks. Yeping Sun-- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] set line_width command doesn't work
Dear all I want to make line presentation in pymol looks more thicker so I enter "set line_width, 3", but the lines in the viewer window don't show any change. Have you meet such circumstance? The pymol (version 1.5.0.1) is installed in centos5.9 system and other functions seem well. Thanks. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] set stick_transparency
Dear all, I want to set transparecy of selected residues which are shown as sticks and I use the command: set stick_transparency, 0.8, sele but it doesn't work. If I use the command: stick_transparency, 0.8 then all sticks become transparency, including the residues I selected and didn't selected. How can I set transparency of selected residues but not non-selected ones? Thanks! Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] 转发:set stick_transparency
Dear all, I want to set transparecy of selected residues which are shown as sticks and I use the command: set stick_transparency, 0.8, sele but it doesn't work. If I use the command: stick_transparency, 0.8 then all sticks become transparency, including the residues I selected and didn't selected. How can I set transparency of selected residues but not non-selected ones? Thanks! Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] residue B factor
Dear pymol users, Pdb files give B factor of each atom. How can I get B factor of the individual residues? Thanks. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences-- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] gradually changed colors with flexibility
Dear all,I want to show amino acids in a structure according to their flexibility (B factor) by gradually changed colors. Can pymol do this? Thanks. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] 答复： gradually changed colors with flexibility
Hi, professor Holder,Thank you for the reply, but how can I do this on the level of individual amino acids in stead of atom? I have two homolog stuctures and I want to map the difference between the b factors of the corresonding residues of these two stuctures rather than individual atoms. And I want to use gradually deepened color from white to blue. Could you explain more in detail? Thanks. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 发件人：Thomas Holder 发送时间：2013年12月10日(星期二) 04:50 收件人：孙业平 抄 送：pymol-users 主 题：Re: [PyMOL] gradually changed colors with flexibility Hi Yeping, use the spectrum command: PyMOL> spectrum b, blue_white_red http://pymolwiki.org/index.php/Spectrum Cheers, Thomas On 09 Dec 2013, at 11:30, sunyeping wrote: > Dear all, > > I want to show amino acids in a structure according to their flexibility (B > factor) by gradually changed colors. Can pymol do this? Thanks. > > Yeping Sun > > Institute of Microbiology, Chinese Academy of Sciences -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net-- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] show atoms as circle
Dear all,I want to draw CA atoms of a peptide as circles, but not spheres. How can I do that? Thanks Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] animation showing conformational change
Dear all,If I have the structures representing two conformations of one protein, then could I make a animation movie that shows how the protein transforms from one conformation to the other conformation using pymol? Thanks. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test & Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] pymol_tube and pymol_loop
Dear all, I want to show my protein in cartoon_tube or cartoon_loop described in pymolwiki ( http://www.pymolwiki.org/index.php/Cartoon), but when I type the command show cartoon_tube, allit returns error information:Error: unknown representation: 'cartoon_tube'. Choices: angles cgo ellipsoids lines ribbon surface callback dashes everything mesh slice volume cartoon dihedrals extent nb_spheres spheres cell dots labels nonbonded sticks So how should I show pymol_tube and pymol_loop? Thanks. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] show color bar with b-factor
Dear all, I am trying to map b factor onto a structure by gradually changing color. I use the following command: pymol>spectrum b, blue_white_red, byres=1It seems to work. But I don't know how to make pymol show a color bar presenting the range of b factor. Could you help me? Thanks.Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] gradually changed colors with b-factor colum
Dear proessor Holder and pymol users,I previously tried to color a protein structure accord to a set of customer data. I replaced the b factor of individual Ca atoms and colored the structure with the command:spectrum b, blue_white_red, byres=1 But I think I need a color scale bar to show the range of the data set. According to PymolWiki (http://www.pymolwiki.org/index.php/Advanced_Coloring#Creating_a_Color_bar), this can be done with the following steps:Create a pdb-file which contains CA positions only, whereas the numbers correspond to your wanted increments of colors. Make CA's to be separated by 5 Angstroem.Load this new pseudobar-pdb file into PyMOL, make bonds between increment 1 and increment 2 [increment 2 and increment 3 and so on...], define/assign a smooth color for each increment (copy colors definition from automatically created colors made by b-factor script) and show the b-factor bar as lines (or sticks).Could you tell me how to assign blue_white_red color for these increment? And if the range of my data set is -0.8 to 2.3, how to make the color gradient reflect this range? Thank you very much. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 发件人：Thomas Holder 发送时间：2013年12月11日(星期三) 12:49 收件人：孙业平 抄 送：pymol-users 主 题：Re: [PyMOL] 答复： gradually changed colors with flexibility Hi Yeping, the spectrum command has a "byres" argument to operate on the residue level: PyMOL>spectrum b, blue_white_red, byres=1 There is no white_blue color ramp, but there is a script which provides this: http://pymolwiki.org/index.php/Spectrumany It doesn't have the byres argument. If you only show cartoon, just limit the selection to CA atoms: PyMOL>run path/to/spectrumany.py PyMOL>spectrumany b, white blue, name CA If you want to show all atoms, you can map the CA atom b-factor to all residue atoms with this script: http://pymolwiki.org/index.php/AlphaToAll Hope that helps. Cheers, Thomas On 10 Dec 2013, at 01:04, sunyeping wrote: > Hi, professor Holder, > > Thank you for the reply, but how can I do this on the level of individual > amino acids in stead of atom? I have two homolog stuctures and I want to map > the difference between the b factors of the corresonding residues of these > two stuctures rather than individual atoms. And I want to use gradually > deepened color from white to blue. Could you explain more in detail? Thanks. > > Yeping Sun > > Institute of Microbiology, Chinese Academy of Sciences > > > -- > 发件人：Thomas Holder > 发送时间：2013年12月10日(星期二) 04:50 > 收件人：孙业平 > 抄 送：pymol-users > 主 题：Re: [PyMOL] gradually changed colors with flexibility > > Hi Yeping, > > use the spectrum command: > > PyMOL> spectrum b, blue_white_red > > http://pymolwiki.org/index.php/Spectrum > > Cheers, > Thomas > > On 09 Dec 2013, at 11:30, sunyeping wrote: > > > Dear all, > > > > I want to show amino acids in a structure according to their flexibility (B > > factor) by gradually changed colors. Can pymol do this? Thanks. > > > > Yeping Sun > > > > Institute of Microbiology, Chinese Academy of Sciences -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net-- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] RE： gradually changed colors with b-factor colum
Dear Jared,Thank you for the reply. But I still have a couple of questions: As for the spectrumbar script, how could I assign a particular data value to a particular color? By using the command:spectrumbar blue, white, redI can get a spectrumbar. If the range of my data is -0.3~2.3, maybe I can label two end of the bar with -0.3 and 2.3 manually, respectively. But if I want to label more data to the bar? How shold I do? As you suggest, I can simplely get a 2D box with a linear gradient fill. But the question is the same with above: how could I correctly label the bar according my data set?Best regards, Yeping-- 发件人：Sampson, Jared 发送时间：2014年4月29日(星期二) 04:36 收件人：孙业平 抄 送：pymol-users 主 题：Re: [PyMOL] gradually changed colors with b-factor colum Hi Yeping - I was about to suggest Sean Law’s new spectrumbar script, but I see he beat me to it. You’ll have to adjust the positioning of the bar with some trial and error. Also, in case you get a “NameError: global name 're' is not defined” error, simply change the 4th line from: from re import * to import re I’ve just submitted a pull request with this fix, but if you download the script before it’s accepted, you'll have to make the change yourself. Alternatively, you could fairly easily create a simple 2D box with a gradient fill in e.g. Inkscape or Illustrator with the appropriate colors and add the labels manually. So long as you specify a linear gradient, it should be fairly consistent with the PyMOL values. Hope that helps. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Apr 27, 2014, at 8:50 AM, sunyeping wrote: Dear proessor Holder and pymol users, I previously tried to color a protein structure accord to a set of customer data. I replaced the b factor of individual Ca atoms and colored the structure with the command: spectrum b, blue_white_red, byres=1 But I think I need a color scale bar to show the range of the data set. According to PymolWiki (http://www.pymolwiki.org/index.php/Advanced_Coloring#Creating_a_Color_bar), this can be done with the following steps: Create a pdb-file which contains CA positions only, whereas the numbers correspond to your wanted increments of colors. Make CA's to be separated by 5 Angstroem.Load this new pseudobar-pdb file into PyMOL, make bonds between increment 1 and increment 2 [increment 2 and increment 3 and so on...], define/assign a smooth color for each increment (copy colors definition from automatically created colors made by b-factor script) and show the b-factor bar as lines (or sticks). Could you tell me how to assign blue_white_red color for these increment? And if the range of my data set is -0.8 to 2.3, how to make the color gradient reflect this range? Thank you very much. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 发件人：Thomas Holder 发送时间：2013年12月11日(星期三) 12:49 收件人：孙业平 抄 送：pymol-users 主 题：Re: [PyMOL] 答复： gradually changed colors with flexibility Hi Yeping, the spectrum command has a "byres" argument to operate on the residue level: PyMOL>spectrum b, blue_white_red, byres=1 There is no white_blue color ramp, but there is a script which provides this: http://pymolwiki.org/index.php/Spectrumany It doesn't have the byres argument. If you only show cartoon, just limit the selection to CA atoms: PyMOL>run path/to/spectrumany.py PyMOL>spectrumany b, white blue, name CA If you want to show all atoms, you can map the CA atom b-factor to all residue atoms with this script: http://pymolwiki.org/index.php/AlphaToAll Hope that helps. Cheers, Thomas On 10 Dec 2013, at 01:04, sunyeping wrote: > Hi, professor Holder, > > Thank you for the reply, but how can I do this on the level of individual > amino acids in stead of atom? I have two homolog stuctures and I want to map > the difference between the b factors of the corresonding residues of these > two stuctures rather than individual atoms. And I want to use gradually deepened color from white to blue. Could you explain more in detail? Thanks. > > Yeping Sun > > Institute of Microbiology, Chinese Academy of Sciences > > > -- > 发件人：Thomas Holder > 发送时间：2013年12月10日(星期二) 04:50 > 收件人：孙业平 > 抄 送：pymol-users > 主 题：Re: [PyMOL] gradually changed colors with flexibility > > Hi Yeping, > > use the spectrum command: > > PyMOL> spectrum b, blue_white_red > > http://pymolwiki.org/index.php/Spectrum > > Cheers, > Thomas > > On 09 Dec 2013, at 11:30,
[PyMOL] paste pictures
Dear all,how can I paste pictures on this pymol mail list? Thanks. Yeping Sun -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] RE： what is the pymol representation in this figure?
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 surface with transparency on, if I'm not getting it wrong.Dear Gianluca,Thank you for the response, but how to set the side chain of the selected residues as solid surface? I used the commandshow surface, selebut the surface appears not like the sample figure in which there seems to be a 3D volume around the sticks representations of the side chains, instead, the surface shown is just a plane aside the sticks representation. So what is the proper way to obtain the effects in the sample figure?Best Regards.Yeping On 7/10/14 12:40 PM, sunyeping wrote: > Dear all, > > Could anyone tell me how the figure attached to the following web site > or the attach file is drawn? In What pymol repersentation of the > residues is shown? > > http://cashero.lingw.net/ > > Yeping Sun > > > > > > -- > Open source business process management suite built on Java and Eclipse > Turn processes into business applications with Bonita BPM Community Edition > Quickly connect people, data, and systems into organized workflows > Winner of BOSSIE, CODIE, OW2 and Gartner awards > http://p.sf.net/sfu/Bonitasoft > > > > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Gianluca Santoni, Dynamop Group Institut de Biologie Structurale 6 rue Jules Horowitz 38027 Grenoble Cedex 1 France _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net-- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] FW： RE： what is the pymol representation in this figure?
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 instruction and then show surface, but the surface is still an incomplete plane, unlike what I wish as in the sample. And I have another question: I show a residue in a helix of cartoon representation as sticks, and give it a color different from the cartoons of the helix, but the new color extented to the helix. How chould I prevent this happening? cartoon_discrete_colors seems doesn't work. Best Regard. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 发件人：Gianluca Santoni 发送时间：2014年7月11日(星期五) 14:59 收件人：孙业平 抄 送：pymol-users 主 题：Re: [PyMOL] RE： what is the pymol representation in this figure? 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 surface with transparency on, > if I'm not getting it wrong. > > Dear Gianluca, > > Thank you for the response, but how to set the side chain of the > selected residues as solid surface? I used the command > > show surface, sele > > but the surface appears not like the sample figure in which there seems > to be a 3D volume around the sticks representations of the side chains, > instead, the surface shown is just a plane aside the sticks > representation. So what is the proper way to obtain the effects in the > sample figure? > > Best Regards. > > Yeping > > On 7/10/14 12:40 PM, sunyeping wrote: > > Dear all, > > > > Could anyone tell me how the figure attached to the following web site > > or the attach file is drawn? In What pymol repersentation of the > > residues is shown? > > > > http://cashero.lingw.net/ > > > > Yeping Sun > > > > > > > > > > > > > -- > > Open source business process management suite built on Java and Eclipse > > Turn processes into business applications with Bonita BPM Community > Edition > > Quickly connect people, data, and systems into organized workflows > > Winner of BOSSIE, CODIE, OW2 and Gartner awards > > http://p.sf.net/sfu/Bonitasoft > > > > > > > > ___ > > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > > -- > Gianluca Santoni, > Dynamop Group > Institut de Biologie Structurale > 6 rue Jules Horowitz > 38027 Grenoble Cedex 1 > France > _ > Please avoid sending me Word or PowerPoint attachments. > See http://www.gnu.org/philosophy/no-word-attachments.html > > -- > Open source business process management suite built on Java and Eclipse > Turn processes into business applications with Bonita BPM Community Edition > Quickly connect people, data, and systems into organized workflows > Winner of BOSSIE, CODIE, OW2 and Gartner awards > http://p.sf.net/sfu/Bonitasoft > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Gianluca Santoni, Dynamop Group Institut de Biologie Structurale 6 rue Jules Horowitz 38027 Grenoble Cedex 1 France _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ PyMOL-users mailing list
[PyMOL] symmetry mates
Dear pymol users, I want to operate a structure whose crystal structure has one molecule in one asymmetry unit. I try to display its polymer. I loaded the structure and used "generate" command in the pymol GUI interface: A>generate>symmetry mates>4A, and then many copies of this molecure appeared but in a quite disoder pattern. According to the paper that published this structure, it is a polymer arranged in a linear pattern. Could you tell me how can I display this linear polymer? Thanks in advance. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] how to get the surface representation look better?
Dear all,Please see the figure (surface1.tif) I deposited in dropbox (https://www.dropbox.com/home, Account sunyep...@aliyun.com, Password: pymolusers). A is taken from a literature, and B is prepared by myself. In A, the stick representation of the side chains of residues P3, D156, R97, etc., is wraped around in a representation that looks like having a transparent stereoscopic volume. I guess this represnetation is some kind of surface. However, in B, although I show the surface represnetation for residue E63, it looks like a curved surface locate aside E63 and doesn't wrap around the side chain of E63 as in A. Could anyone tell me how the effect of the surface representation (if I am correct) was prepared? Best regards. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] chain ID in oligomer obtained by symmetry operation
Dear all,I have the pdb file of a protein which contains one chain and the chian ID is "A". By symmetry operation of pymol I got an oligomer and save it as a new pdb file. However when I open the pdb file of the oligomer in pymol again, only one chain is display. I think it may caused by the clash of the chain IDs: the IDs of all chains in the the pdb file of the oligomer are "A". I changed IDs of the secend and third and other chains to "B", "C", "D", etc., and this seemed to work. Is there a way to automatically change the chain IDs in pymol when saving the oligomer structure in such a circumstance?Best regards.Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] naming of chain id
I have a protein which contains 32 chains. By using A-Z can only name 26 chains. Can I use expression containing two character such as A1, AB, etc. to as chain id? Will this change the format of the pdb files? Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] cartoon and line representation
Dear all I want to display structures which contains numerous chains such as viruses in pymol. I find these sturctures can be displayed normally as line representation. However, when I show them as cartoon, usually only one chain can be displayed, and usually it is cartoon loop rather than the normal cartoon. It there any way to display the whole structute as cartoon? For example, I display the HBV capsid in pymol by the follow commands: fetch 3j2v, type=pdb1, async=0 split_states 3j2v delete 3j2v orientThe whole virus capsid appeared as line representation. Then I type: Hide everythingshow cartoonOnly one chain shown as cartoon loop in pymolThanks in advance. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] re： cartoon and line representation
Dear Jared,I am using Open Source PyMOL 1.6.0.0. If you save the whole virus structure as a single pdb file, and reload it into pymol and then show it as cartoon, can you still display the whole structure? As for me, it can display only one chain shown as cartoon_loop.Best regards. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 发件人：Sampson, Jared 发送时间：2014年9月2日(星期二) 22:23 收件人：孙业平 抄 送：pymol-users 主 题：Re: [PyMOL] cartoon and line representation Hi Yeping - I’m unable to reproduce the behavior you’re seeing—using your commands in Open Source PyMOL 1.7.2.0, I get the whole capsid displayed properly as a cartoon. What version of PyMOL are you using? You could also try using the `all_states` setting instead: fetch 3j2v, type=pdb1, async=0 set all_states, 1 orient as cartoon I am using Open Source PyMOL 1.6.0.0. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Sep 2, 2014, at 6:20 AM, sunyeping wrote: Dear all I want to display structures which contains numerous chains such as viruses in pymol. I find these sturctures can be displayed normally as line representation. However, when I show them as cartoon, usually only one chain can be displayed, and usually it is cartoon loop rather than the normal cartoon. It there any way to display the whole structute as cartoon? For example, I display the HBV capsid in pymol by the follow commands: fetch 3j2v, type=pdb1, async=0 split_states 3j2v delete 3j2v orient The whole virus capsid appeared as line representation. Then I type: Hide everything show cartoon Only one chain shown as cartoon loop in pymol Thanks in advance. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] can pymol make movie for MD trajectory?
Dear all, Can pymol make a movie from the trajectory file of molecular dynamics ( dcd file from NAMD simulation or trr file from GROMACS MD simulation) that contains several thousands of frames? and how?Best regards. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] color a polypeptide continuously
Dear pymol user,Could you tell me how to color a polypeptide continuously from N- to C-terminal by continuous spectrum such as red to blue? Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] The angle between two subunit of a protein
Dear all,I have a protein complex which contains two subunit. How can I measure the angle between these to subunit? Thanks Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] determine symmetry of a protein
Dear pymol user,I have a homoligomer protein composed of several same subunits. How can I know the symmetry of it (whether it has 2, 3 or 6-fold symmetry)? Can pymol determine this property of the protein?Best regards,Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] sticks do not connect to the backbone
Dear all, I find that when I show the protein as cartoon representation in pymol, and select some residues to show as sticks, then the sticks do not connect to the backbone shown by the cartoon but looks as floating over the backbone. How to make the sticks connect to the backbone? With many thanks. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences-- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] how to highlight some residues and make other residues being as background?
Dear all,In order to emphasize local interactions of several residues within a protein, I want to highlight these studied residues but make other residues vague and being as background. The setting "set fog, on" doesn't help much because the constrast between the studied residues and other residues is not strong. Could you help me with this problem? With many thanks.Yeping Sun Institute of Microbiology, Chinese Academy of Sciences-- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] How to name overfull chains in PDB file?
Dear all, I now have some problems in naming the chains in PDB files. If a PDB file contains more than 26 chains, say, 40 chains, I can name the first 26 chains with the letters "A" to "Z", but how should I name the rest 14 chains？ It seems that they can not be named with repeated letters which have been used because this cause abnormality in display function in pymol. And identifier like "A1", "A2", etc, can not be used either because there is only one colum (colum 22) for the chain ID in PDB file format. So what is the proper way to name the chains for this circumstance? Thanks in advance.Yeping Sun Institute of Microbiology, Chinese Academy of Sciences-- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] how to measure the angle between two protein complexes
Dear all, I have a protein complex which has a ring-like shape; and another protein complex which forms a long filament. Is there a way in Pymol to measure the angle between the ring plane and the filament? Best regards. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences-- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] How to highlight the interactions between two proteins consituting the complex?
Dear pymol users, I wish to highlight the interactions between two proteins consituting the complex. I want to make these interacting residues clear but other residues obscure as the background in Pymol. Which would be the skill? Thanks a lotYeping Sun Institute of Microbiology, Chinese Academy of Sciences-- Monitor Your Dynamic Infrastructure at Any Scale With Datadog! Get real-time metrics from all of your servers, apps and tools in one place. SourceForge users - Click here to start your Free Trial of Datadog now! http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Why does the right button of the mouse cannot change the size of the image?
Dear pymol user, I find my pymol install in win7 system have some problems on the right button of the mouse. It cannot change the size of the the image in the Pymole viewer window; instead, when I click right botton of the mouse and drag, the size of the pymol viewer window changes: dragging the mouse down or up, the pymol viewer window becomes minized or maximaized, while dragging the mouse to the left or the right, the pymol viewer window goes to the left or the right of the computer screen. It is very strange and troubling. Did anyone experiencing this and how to fix it? Thank you in advance! Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Why does the right button of the mouse cannot change the size of the image?
Dear pymol user, I find my pymol installed in win7 system have some problems on the right button of the mouse. It cannot change the size of the the image in the Pymol viewer window; instead, when I click right botton of the mouse and drag, the size of the pymol viewer window changes: dragging the mouse down or up, the pymol viewer window becomes minized or maximaized, while dragging the mouse to the left or the right, the pymol viewer window goes to the left or the right of the computer screen. It is very strange and troubling. Did anyone experience this and how to fix it? Thank you in advance! Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] How to make a movie that show competitive bindings between proteins?
Dear all, I wish to make a movie which shows the following scenary: firstly two subunits of a complex form the complex, and then another protein appears, competitively bind to one subunit of that complex and substitutes the other subunit. I guess only pymol might not be able to do these. Could anyone give me some guidance? Best regards.Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] how to rotate a subdomain?
Dear all,Could it be possible to move or rotate a subdomain of one peptide chain around a hinge manually in pymol?Thanks in advance! Yeping SunInstitute of Microbiology, Chinese Academy of Sciences-- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] show the long helix filament
Dear all,I am studying a published protein molecule which was claimed to be helical symmetric. The pdb file contain 3 copies of this molecule arranged in head-to-tail patern. The author claims that this interation is repeated in a directional manner along the P31 screw axis. Does anyone know how to show the whole long helix filament rather that just three protomer of this molecule? Can pymol do this?Best regards.Yeping SunInstitute of Microbiology, Chinese Academy of Sciences-- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] How to show one side of the surface of an object
Dear all, If we show surface of an object in pymol, the surface appears to wrap the object all around. But whether is it possible to show a surface that cover only one side of certain part of that object？ For example, when I draw a surface of the active site that contacts a drug, I wish the surface should look like a curved surface without a thickness suspending over the active residues instead of a volume that wraps all directions of the the active site residues. I remember I saw such figures somewhere but I cann't find them now? Do you have any idea how draw it? Thanks a lot. Yeping Sun -- Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] how to judge the favorability of a residue to another residue and a group of residues?
Dear all, Do you have any idea of how to judge the favorability of a residue to another residue and a group of residues. I mean I conceptually know that two hydrophobic residue repel each other, and two residues with the same charge repel each other, but is there any comprehensive and precise principal or quatitative algorithms to describe this problem? Best regards, Yeping Sun-- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Install problem
Dear all,
I am trying to install pymol on my centos 6 system from source following the
guide on the pymolwiki ("https://pymolwiki.org/index.php/Linux_Install)". The
installation process seemed to be successful but when I initialized pymol, I
got the following error:
import _tkinter # If this fails your Python may not be configured for Tk
ImportError: libtk8.6.so: cannot open shared object file: No such file or
directory.
How could I solve the problem?
I'll appreciate any help!
Best regards.
Yeping Sun
--
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[PyMOL] Error aroused when install pymol from source
Dear pymol users, I am trying to intall pymol on my centos 7 system from source using the mothed discribed at pymolwiki (https://pymolwiki.org/index.php/Linux_Install)Everything was ok until I run install script: #!/bin/bash -e prefix=/opt/pymol-svn modules=$prefix/modules # If you want to install as root, then split this line up in "build" # and "install" and run the "install" with "sudo" python2.7 setup.py build install \ --home=$prefix \ --install-lib=$modules \ --install-scripts=$prefix I got a error message and the installation process was terminated: In file included from contrib/mmtf-c/mmtf_parser.cpp:31:0: contrib/mmtf-c/mmtf_parser_private.h:38:23: fatal error: msgpack.hpp: No such file or directory #include ^ compilation terminated. I then installed msgpack by yum command and tried to run the pymol install script again, but the same error still occurred. I googled this problem but cannot find a answer. Could anyone help me here? Best regards. Yeping Sun-- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] how to make selected residues blurry?
Dear all, Could you please check this figure at the following link? https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are: residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command: set transparency, 0.8, sele but it doesn't work. Could anyone help me figure it out？ With sincere thanks. Arthur___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] how to make selected residues blurry?
Dear all, Could you please check this figure at the following link? https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are: residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command: set transparency, 0.8, sele but it doesn't work. Could anyone help me figure it out？ With sincere thanks. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] how to make selected residues blurry?
Hi, Paul, Thank you for your reply. I think the ‘set transparency’ command is on the correct direction, but there is another problem. In order to apply the ‘set transparency’, we should use "create" or "extract" command to make a new objective for the selected atoms. However, after I select the atoms that I want to make transparent, and use the command "extract": extract new_obj, sele I find the new object is broken from the rest part of the structure. And then I use the commend: set cartoon_transparency, 0.7, new_obj The breaking between the new objective (the transparent part) and the rest part become more obvious. Please see the figure at the line (https://drive.google.com/file/d/1XQqGeN7JRLfSlexk4J7ufESWhnTJM3bW/view?usp=sharing). Could you help me with the "breaking" problem? Best regards, Yeping -- From:Smith, Paul Send Time:2018 Dec 3 (Mon) 20:38 To:孙业平 ; pymol-users Subject:RE: [PyMOL] how to make selected residues blurry? Hi, The ‘set transparency’ command will set the transparency of a surface (e.g. the interface between a protein and the surrounding water). I think the command you’re after is ‘set cartoon_transparency’ (https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels). Depending on your choice of representation, see also ‘set sphere_transparency’ and ‘set stick_transparency’. Cheers, Paul From: sunyeping via PyMOL-users Sent: 03 December 2018 03:02 To: pymol-users Subject: [PyMOL] how to make selected residues blurry? Dear all, Could you please check this figure at the following link? https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are: residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command: set transparency, 0.8, sele but it doesn't work. Could anyone help me figure it out？ With sincere thanks. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] how to make selected residues blurry?
Hi Paul, Now I get closer to the final anwer! After following your steps, I get the effect I want. However, afer I "ray" the structure, a small part of the structure which I don't mean to set transparent become blur. Please see the image in the red circle in fig-3 (https://drive.google.com/file/d/1Au0LUkRKMCBCtN7XM_O0WlGKLhmtnyMV/view?usp=sharing). How does that happen and how to fix it? Thank you again and best regards. Yeping -- From:Smith, Paul Send Time:2018 Dec 4 (Tue) 21:00 To:孙业平 ; pymol-users Subject:RE: [PyMOL] how to make selected residues blurry? Hi Yeping, To avoid this ‘breaking’ of your protein you will first need to create a copy of the entire molecule, set the transparency of the copy to your desired value, then hide the residues you want to make transparent on your original object. So, you will do something like this: # create a copy of your original object: create new_obj, # set all residues on the copy to be transparent: set cartoon_transparency, , new_obj # hide the residues you wish to be transparent on your original object: select hide, cartoon_skip, hide and This should prevent the your molecule from appearing to be broken. Cheers, Paul From: sunyeping Sent: Tuesday, December 4, 2018 3:23:00 AM To: pymol-users; Smith, Paul Subject: Re: [PyMOL] how to make selected residues blurry? Hi, Paul, Thank you for your reply. I think the ‘set transparency’ command is on the correct direction, but there is another problem. In order to apply the ‘set transparency’, we should use "create" or "extract" command to make a new objective for the selected atoms. However, after I select the atoms that I want to make transparent, and use the command "extract": extract new_obj, sele I find the new object is broken from the rest part of the structure. And then I use the commend: set cartoon_transparency, 0.7, new_obj The breaking between the new objective (the transparent part) and the rest part become more obvious. Please see the figure at the line (https://drive.google.com/file/d/1XQqGeN7JRLfSlexk4J7ufESWhnTJM3bW/view?usp=sharing). Could you help me with the "breaking" problem? Best regards, Yeping -- From:Smith, Paul Send Time:2018 Dec 3 (Mon) 20:38 To:孙业平 ; pymol-users Subject:RE: [PyMOL] how to make selected residues blurry? Hi, The ‘set transparency’ command will set the transparency of a surface (e.g. the interface between a protein and the surrounding water). I think the command you’re after is ‘set cartoon_transparency’ (https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels). Depending on your choice of representation, see also ‘set sphere_transparency’ and ‘set stick_transparency’. Cheers, Paul From: sunyeping via PyMOL-users Sent: 03 December 2018 03:02 To: pymol-users Subject: [PyMOL] how to make selected residues blurry? Dear all, Could you please check this figure at the following link? https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are: residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command: set transparency, 0.8, sele but it doesn't work. Could anyone help me figure it out？ With sincere thanks. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] how to make selected residues blurry?
Hi Jared,
Your solution is very clever and helpful, but I don't know how to use the
set_view command. I think it is vey important here because after this setting
the scene becomes very close to the original figure in the paper. Could you
explain how do you set the 18 float numbers?
Thank you very much and best regards.
Yeping
--
From:Jared Sampson
Send Time:2018 Dec 6 (Thu) 12:09
To:孙业平
Cc:pymol-users ; "Smith, Paul"
Subject:Re: [PyMOL] how to make selected residues blurry?
Hi Yeping -
I had replied to your first email (on 11/30) with a similar suggestion to
Paul's of using the `cartoon_transparency` setting, but now after looking at
the original figure you're trying to replicate more closely, I realize that
there isn't actually any transparency in that figure at all!
The authors achieved this effect simply by using lighter and darker shades of
("palecyan" and "deepteal") for the hemagglutinin chain. The following script
reproduces the original figure you shared almost exactly.
bg_color white
fetch 4gms, async=0
# hemagglutinin selections
select ha, chain A
select l130, ha and resi 133-138
select l150, ha and resi 155-163
select h190, ha and resi 187-196
select l220, ha and resi 225-228
select loops, l130 or l150 or h190 or l220
# antibody selection
select h2, chain H and resi 51-59
deselect
# basic view
hide everything
as cartoon, ha
as cartoon, h2
cartoon tube
# colors
color orange, h2
color palecyan, ha
color deepteal, loops
set_view (\
-0.718157351,0.514449000, -0.468602538,\
-0.667115033, -0.317360103,0.673974276,\
0.198008969,0.796632588,0.57977,\
0.45628, -0.60942, -75.169761658,\
20.388980865, -23.567779541, 38.543788910,\
52.026283264, 98.326217651, -20.0 )
set ray_opaque_background, 1
ray 800, 800
I've uploaded the resulting image (with the script in the description) to
PyMOL wiki: https://pymolwiki.org/index.php/File:4gms_colors.png
Hope that helps.
Cheers,
Jared
On December 5, 2018 at 3:33:35 AM, sunyeping via PyMOL-users
(pymol-users@lists.sourceforge.net) wrote:
Hi Paul,
Now I get closer to the final anwer!
After following your steps, I get the effect I want. However, afer I "ray" the
structure, a small part of the structure which I don't mean to set transparent
become blur. Please see the image in the red circle in fig-3
(https://drive.google.com/file/d/1Au0LUkRKMCBCtN7XM_O0WlGKLhmtnyMV/view?usp=sharing).
How does that happen and how to fix it?
Thank you again and best regards.
Yeping
--
From:Smith, Paul
Send Time:2018 Dec 4 (Tue) 21:00
To:孙业平 ; pymol-users
Subject:RE: [PyMOL] how to make selected residues blurry?
Hi Yeping,
To avoid this ‘breaking’ of your protein you will first need to create a copy
of the entire molecule, set the transparency of the copy to your desired value,
then hide the residues you want to make transparent on your original object.
So, you will do something like this:
# create a copy of your original object:
create new_obj,
# set all residues on the copy to be transparent:
set cartoon_transparency, , new_obj
# hide the residues you wish to be transparent on your original object:
select hide,
cartoon_skip, hide and
This should prevent the your molecule from appearing to be broken.
Cheers,
Paul
From: sunyeping
Sent: Tuesday, December 4, 2018 3:23:00 AM
To: pymol-users; Smith, Paul
Subject: Re: [PyMOL] how to make selected residues blurry?
Hi, Paul,
Thank you for your reply. I think the ‘set transparency’ command is on the
correct direction, but there is another problem. In order to apply the ‘set
transparency’, we should use "create" or "extract" command to make a new
objective for the selected atoms. However, after I select the atoms that I want
to make transparent, and use the command "extract":
extract new_obj, sele
I find the new object is broken from the rest part of the structure. And then I
use the commend:
set cartoon_transparency, 0.7, new_obj
The breaking between the new objective (the transparent part) and the rest part
become more obvious. Please see the figure at the line
(https://drive.google.com/file/d/1XQqGeN7JRLfSlexk4J7ufESWhnTJM3bW/view?usp=sharing).
Could you help me with the "breaking" problem?
Best regards,
Yeping
--
From:Smith, Paul
Send Time:2018 Dec 3 (Mon) 20:38
To:孙业平 ; pymol-users
Subject:RE: [PyMOL] how to make selected residues blurry?
Hi,
The ‘set transparency’ command will set the transparency of a surface (e.g. the
interface between a protein and the surrounding water). I think the command
you’re after is ‘set cartoon_transparency’
(https://pymolwiki.org/index.php/Cartoon#Various_T
[PyMOL] How to make protein blur but keep ligand clear?
Dear all, I have a protein-ligand complex and I wish to make the protein looks blur but keep the ligand clear and sharp with pymol. I find a "focalblur" script (https://pymolwiki.org/index.php/FocalBlur) which seems to be able to do this. However I can get the fancy effect illustrated in the examples of the wiki for this script. With the follow command: FocalBlur aperture=2,samples=10,ray=1,width=1000,height=1000 I just make the ligand rather the the protein become blur (Please see the image at https://drive.google.com/open?id=1qzXDLzVyxI85sJ8H6Zhv8pd8Cq7rA18U, and the pse file used to make this image is availabe at https://drive.google.com/open?id=1Gjrl5ePifadWEK8-AZYVXY7yX07kOLF7). Could anyone help with this？ What does the argument "aperture" do? How to control which part become blur? Is there better way to make the ligand blur? Thank you very much! Arthur___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to show the boundary of each selected residues in surface presentation with pymol
Dear everyone, It there a way to show the boundary of each selected residues in surface presentation with pymol? Best regards Arthur___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to assign secondary structure as 3-10 helix in pymol?
Dear pymol user, I wonder why sometimes the secondary structure of a protein can not be displayed incorrect in pymol. I have a structure, some residues are predicted to be sheet or 3-10 helix with DSSP, but they are displayed as loop. Only typing "dss" command in pymol doesn't work. I know by using the "alter" commad the secondary structures can be assigned. The following command: alter 61-63/, ss='S' can assign residue 61-63 as sheet. However, what is the command to assign residues as 3-10 helix? Thank you in advance. Arthur___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol?
Thank you for the reply. Do alter and rebuild commands really change the secondary structure of the specific residues or they just change the display? I saved the structure altered bt the alter and rebuild commands, but when I open the structure agian in pymol, the residues I changes are still displayed as in the original structure file. Best regards -- From:h. adam steinberg Sent At:2019 Jun. 5 (Wed.) 20:43 To:孙业平 ; pymol-users Subject:Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol? It’s the same command but just change the “S” to an “H”. Or you can use a “L” if you want a loop (unstructured). alter 3-10/, ss=‘H’ You also need to enter the command: rebuild, to redraw the structure on your screen. Use rebuild after you enter the alter command. On Jun 4, 2019, at 10:37 PM, sunyeping via PyMOL-users wrote: Dear pymol user, I wonder why sometimes the secondary structure of a protein can not be displayed incorrect in pymol. I have a structure, some residues are predicted to be sheet or 3-10 helix with DSSP, but they are displayed as loop. Only typing "dss" command in pymol doesn't work. I know by using the "alter" commad the secondary structures can be assigned. The following command: alter 61-63/, ss='S' can assign residue 61-63 as sheet. However, what is the command to assign residues as 3-10 helix? Thank you in advance. Arthur___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] "Qt not available, using GLUT/Tk interface" error
Dear all, I installed pymol according to guide at https://pymolwiki.org/index.php/Linux_Install. When I launched pymol, and get the "Qt not available, using GLUT/Tk interface" error and no pymol GUI appeared. How could I deal with this problem? Best regards___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to color stick and surface representation separately
Dear all, I color a protein as blue, display it by surface and cartoon simultaneously, and set the surface transperant so that the cartoon representation inside the surface can be seen. I display one residue as stick. I want to color the stick by element, but keep the surface representation as blue. However, I don't know how to do this. I can color the residue (please see the Gln in the yellow circle at https://drive.google.com/open?id=1bviFQGUKgqLdbE-cUNDtzDZSdabc0N4Z), but both the stick and the surface representations are colored by element. Could anyone tell me how to color stick representation of this Gln by element but keep its surface representation as blue? Thank you in advance Yeping___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to color stick and surface representation separately
Hi, Thank you. I think a third method is to create a new object of the protein and display the stick in this new object, and display surface of the original object, so I can color them separately. Best regards -- From:Saurabh Gayali Sent At:2019 Jul. 6 (Sat.) 18:20 To:孙业平 Cc:pymol-users Subject:Re: [PyMOL] How to color stick and surface representation separately there are two ways to achieve this (might not be correct ways, but it will give you results) 1. Open the molucule and choose show as Surface [image.png] This will show complete molecule as a surface. Remember choosing show as surface after choosing line or cartoon will remove former from viewport. - Now choose parts you want to keep and color them before moving on to next part Next select the same molecule and enable line [image.png] remember to not choose line in show as menu but directly from show menu This will keep the old object and add the new line visualization. This way you can show both custom color surface and default color of line/cartoon this way has limitation that you cannot color the second scheme but have to use the default coloring way. 2. Copy the molecule you want to load and create a copy in the folder Load both moleculaes [You won't even need to align them] now You can choose any visualization for both moleculaes as they are separate files. Regards,Saurabh Gayali - I’m protected online with Avast Free Antivirus. Get it here — it’s free forever. On Sat, Jul 6, 2019 at 2:29 PM sunyeping via PyMOL-users wrote: Dear all, I color a protein as blue, display it by surface and cartoon simultaneously, and set the surface transperant so that the cartoon representation inside the surface can be seen. I display one residue as stick. I want to color the stick by element, but keep the surface representation as blue. However, I don't know how to do this. I can color the residue (please see the Gln in the yellow circle at https://drive.google.com/open?id=1bviFQGUKgqLdbE-cUNDtzDZSdabc0N4Z), but both the stick and the surface representations are colored by element. Could anyone tell me how to color stick representation of this Gln by element but keep its surface representation as blue? Thank you in advance Yeping___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe image.png Description: Binary data image.png Description: Binary data ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to label secondary structures in pymol
Dear all, Is it possible to label secondary structures directly in pymol? I mean add a text near local structures which tells the types and numbers of their secondary structures, such as "α1", "β1", "α2", "β2", etc.. Thank you in advance.___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to label secondary structures in pymol
Thank you, Jared. -- From:Jared Sampson Sent At:2019 Jul. 8 (Mon.) 12:08 To:pymol-users ; 孙业平 Subject:Re: [PyMOL] How to label secondary structures in pymol Hi sunyeping - Yes, it is possible. You can pick one atom to label in each SS element. See this old thread: https://sourceforge.net/p/pymol/mailman/message/30823352/. You can also adjust the label position/size/style using the various label settings as well. I would normally direct you to the label wiki page, but that appears (at least to me) to be broken at the moment. So here, instead, is a link to a few-years-old archive of that page. Hope that helps. Cheers, Jared On July 7, 2019 at 1:38:15 PM, sunyeping via PyMOL-users (pymol-users@lists.sourceforge.net) wrote: Dear all, Is it possible to label secondary structures directly in pymol? I mean add a text near local structures which tells the types and numbers of their secondary structures, such as "α1", "β1", "α2", "β2", etc.. Thank you in advance. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to calculate RMSD among multiple proteins
Dear all, It is easy to evaluate the simularity of two proteins in pymol. We just need to align them and a RMSD will be given in pymol. However, I want to compare the strutural similiarity of multiple proteins. I can align two of them once and by doing alignment many times, I can finally get pair-wise RMSD of these proteins. Is there any simple method to do? Is there a scriipt that can automatically calculate the pair-wise RMSD among many proteins in pymol? Thank you in advance. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] The 'select' command for complex residue selection
Dear all, In pymol I loaded two protein: protein_A and protein_B. I want to make a selection of some incontinuous residues from two chains of protein_A, for example, residue 30-34, 71-74 and 117-120 from chain A and residue 88-96 from chain C. How should I write the select command? I tried the following: select sele, (protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119)) or (protein_A and chain C and resi 87-95） but it returns syntax error. So what is the correct command for this? Thank you in advance___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] The 'select' command for complex residue selection
Hi, Ali, Your command format works well. Thank you. -- From:Ali Kusay Sent At:2019 Jul. 9 (Tue.) 11:11 To:孙业平 Cc:pymol-users Subject:Re: [PyMOL] The 'select' command for complex residue selection Hi Sunyeping, I am not sure where your error is coming from (I noticed you also wrote protein_A in second selection as well). I have however rewritten the command in a simpler way, so try this: select sele, (protein_A and c. A and resi 29-33+70-73+116-119) or (protein_B and c. C and resi 87-95) c. A is equivalent to chain A and this residue selection formats avoid the need of annoying “or” statements Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist The University of Sydney School of Pharmacy | Faculty of Medicine and Health 424, Brain and Mind Centre | The University of Sydney | NSW 2050 Email: akus8...@uni.sydney.edu.au From: sunyeping via PyMOL-users Reply-To: sunyeping Date: Tuesday, 9 July 2019 at 12:41 pm To: pymol-users Subject: [PyMOL] The 'select' command for complex residue selection Dear all, In pymol I loaded two protein: protein_A and protein_B. I want to make a selection of some incontinuous residues from two chains of protein_A, for example, residue 30-34, 71-74 and 117-120 from chain A and residue 88-96 from chain C. How should I write the select command? I tried the following: select sele, (protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119)) or (protein_A and chain C and resi 87-95） but it returns syntax error. So what is the correct command for this? Thank you in advance ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] about cealign and align
Dear all, I am now trying to compare two structures by alignment in pymol. The two proteins are similar structures from the same family with about 500 residues. I find that the "cealign" command gives much better result that the "align" command. With the "cealign" command, the two structures aligned well, but with "align" command two structure don't aligned well. The rmsd value given with the "cealign" is much smaller than that given with the "align". However, when I try the align a small region of the two structures, I get the reverse result. I create new objects corresponding to the small region I am interested in from the two whole proteins, respectively and align the two new objects with "align" and "cealign". I find the rmsd value given with "align" is much smaller that than given with "cealign". I wish know the work principle behind "align" and "celign", the calculation formula of them and what cause the difference between aligning the whole proteins and small regions. Could you help me with these? Best regards.___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] how to delete frames from a trajectory loaded by the "load_traj" command?
Dear all, I loaded a gromacs trajetory containing about 1000 frames by the following command in pymol: load protein.gro load_traj protein.xtc I want to use these frames to make a movie. However, I find that the position of the protein in first frame is very different from the other frames some I want to delete the first frame so the protein stays in the same position in all frame. Could you tell me the command of removing the first frame? Thank you. Best regards. Yeping Sun___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] APBS "%x format: an integer is required, not float" error in pymol installed with python 3.7 and "Qt not available, using GLUT/Tk interface" error
Dear everyone, I am trying to use the APBS plugin in pymol to calculate protein electrostatic potentials. My system is centos 7. The pymol was installed with python 3.7 (~/software/build/anaconda3/bin/python). When I try to lauch the APBS Tool 2.1 from the plugin menu of pymol, a window jumps out which reads: "%x format: an integer is required, not float". I've googled it and learned that this error may related to python version. So I try to swith to pymol installed with python2.7 (/usr/bin/python) I install pymol following the guide at https://pymolwiki.org/index.php/Linux_Install, with the command: /usr/bin/python setup.py install --prefix=~/software/pymol/pymol-python2.7-install After the installation finished, I tried to lauch pymol, but meet the error: Qt not available, using GLUT/Tk interface Traceback (most recent call last): File "/home/sunyp/software/pymol/pymol-python2.7-install/lib64/python2.7/site-packages/pymol/__init__.py", line 65, in pymol.launch(args) File "/home/sunyp/software/pymol/pymol-python2.7-install/lib64/python2.7/site-packages/pymol/__init__.py", line 436, in launch _cmd.runpymol(_cmd._get_global_C_object(), block_input_hook) NotImplementedError: compile with --glut Acturally the PyQt4 have been install in my system, I don't understand why it is not available by pymol. And why pymol installed with python3.7 doesn't have such a problem. Even if I reinstall pymol with --glut option: /usr/bin/python setup.py --glut build install --prefix=~/software/pymol/pymol-python2.7-install the same error still comes out. Could you help me with this problem? Thank you in advance. Best regards___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?
Dear everyall, I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames and a reference structure (B.pdb) into pymol. I wish to get the rmsd value between each state of the MD simulation trajectory and the reference structure, but I don't know how. I can use the align command as: "align A, B", but this only gives one rmsd value. Could you tell me how to get the rmsd value between each state of the MD simulation trajectory and the reference structure?___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?
Hello Mateusz,
Thank you very much for your reply to my inquiry. Before I try the PyMOL
extension you mentioned, I want to try scripting language in pymol. I wrote a
attemptive one (align.py):
cmd.load("A.gro")
cmd.load("A.xtc")
cmd.load("ref.pdb")
for i in range(1, 5001):
cmd.align(ref, A,target_state=i)
I ran it in pymol command line, but it doesn't work. I am new to pymol
scripting. Could you write a correct one for me? Thank you very much.
Best regards,
Yeping
--
From:Mateusz Bieniek
Sent At:2019 Aug. 19 (Mon.) 20:32
To:孙业平
Cc:pymol-users
Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD simulation
trajectory and a reference structure?
Hi Sunyeping,
Besides using the scripting language in pymol, you might want to consider the
experimental PyMOL extension created by the PyMOL Fellows (me and Paul Smith,
https://pymol.org/fellowship/). The extension relies on the MDAnalysis package
and so far includes RMSD as an example. Here is the link to the right github
branch https://github.com/bieniekmateusz/pymol-open-source/tree/fellows_mp_2018
If you compile it, you can use the RMSD this way:
mda_load systemX.gro
mda_load_traj systemX.xtc
mda_rmsd
Kind Regards,
Mateusz
On Mon, 19 Aug 2019 at 12:53, sunyeping via PyMOL-users
wrote:
Dear everyall,
I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames and
a reference structure (B.pdb) into pymol. I wish to get the rmsd value between
each state of the MD simulation trajectory and the reference structure, but I
don't know how. I can use the align command as: "align A, B", but this only
gives one rmsd value. Could you tell me how to get the rmsd value between each
state of the MD simulation trajectory and the reference
structure?___
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Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?
Hello Mat,
Thank you for your reply.
I followed your codes in the second line and get a series of output, which look
like:
(9.949092864990234, 267, 0, 9.949092864990234, 267, 420.0, 226)
I guess the first and the fourth float numbers are the rmsd, but what are other
numbers in the line?
Best regards.
Yeping
--
From:Istvan Kolossvary
Sent At:2019 Aug. 20 (Tue.) 00:29
To:Mateusz Bieniek
Cc:孙业平 ; pymol-users
Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD simulation
trajectory and a reference structure?
Superpose all states of an object to one of the states.
print cmd.intra_fit("my-trajCA", 1)Do the same, but this time the
target/reference is a different object.
for s in range(cmd.count_states()): print(cmd.align('my-traj', 'ref',
mobile_state=s + 1, target_state=1, cycles=0, transform=0))
On Mon, Aug 19, 2019 at 9:25 AM Mateusz Bieniek wrote:
There is also intra_rms and instra_fit commands:
https://pymol.org/pymol-command-ref.html#intra_rms
https://pymol.org/pymol-command-ref.html#intra_fit
For example:
intra_fit name CA and resid 1326-1350, 0
Maybe they will be useful.
Best, Mat
On Mon, 19 Aug 2019 at 13:54, sunyeping wrote:
Hello Mateusz,
Thank you very much for your reply to my inquiry. Before I try the PyMOL
extension you mentioned, I want to try scripting language in pymol. I wrote a
attemptive one (align.py):
cmd.load("A.gro")
cmd.load("A.xtc")
cmd.load("ref.pdb")
for i in range(1, 5001):
cmd.align(ref, A,target_state=i)
I ran it in pymol command line, but it doesn't work. I am new to pymol
scripting. Could you write a correct one for me? Thank you very much.
Best regards,
Yeping
--
From:Mateusz Bieniek
Sent At:2019 Aug. 19 (Mon.) 20:32
To:孙业平
Cc:pymol-users
Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD simulation
trajectory and a reference structure?
Hi Sunyeping,
Besides using the scripting language in pymol, you might want to consider the
experimental PyMOL extension created by the PyMOL Fellows (me and Paul Smith,
https://pymol.org/fellowship/). The extension relies on the MDAnalysis package
and so far includes RMSD as an example. Here is the link to the right github
branch https://github.com/bieniekmateusz/pymol-open-source/tree/fellows_mp_2018
If you compile it, you can use the RMSD this way:
mda_load systemX.gro
mda_load_traj systemX.xtc
mda_rmsd
Kind Regards,
Mateusz
On Mon, 19 Aug 2019 at 12:53, sunyeping via PyMOL-users
wrote:
Dear everyall,
I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames and
a reference structure (B.pdb) into pymol. I wish to get the rmsd value between
each state of the MD simulation trajectory and the reference structure, but I
don't know how. I can use the align command as: "align A, B", but this only
gives one rmsd value. Could you tell me how to get the rmsd value between each
state of the MD simulation trajectory and the reference
structure?___
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[PyMOL] How to manually define the lower and upper limit of vacuum electrostatics?
Dear all, I am trying to compare the vacuum electrostatics of three related proteins. I loaded them in pymol and use "Action>generate>vacuum electrostatics menu to generate the vacuum electrostatics of the three proteins. I find that the lower and upper limit of the gradient bars generated with the vacuum electrostatics of the three proteins are different. They are -64.1~64.1, -72.2~72.2 and -82.2~82.2, respectively. I wonder whether I could define the lower and upper limit of the gradients to the same values so that the vacuum electrostatics of the three proteins can be better compared? Best regards. Yeping___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to manually define the lower and upper limit of vacuum electrostatics?
Hello, Marko, Think you for your reply. I can use the bar object "Action" > "Levels" to set the levels/scales to -100~100, but could you tell me what are the units for the values? Best regards -- From:Marko Hyvonen Sent At:2019 Sep. 12 (Thu.) 15:58 To:pymol-users Subject:Re: [PyMOL] How to manually define the lower and upper limit of vacuum electrostatics? Hi Yeping, Click on the bar object "Action" > "Levels" for a few preset levels/scales. hth, Marko On 12/09/2019 08:03, sunyeping via PyMOL-users wrote: Dear all, I am trying to compare the vacuum electrostatics of three related proteins. I loaded them in pymol and use "Action>generate>vacuum electrostatics menu to generate the vacuum electrostatics of the three proteins. I find that the lower and upper limit of the gradient bars generated with the vacuum electrostatics of the three proteins are different. They are -64.1~64.1, -72.2~72.2 and -82.2~82.2, respectively. I wonder whether I could define the lower and upper limit of the gradients to the same values so that the vacuum electrostatics of the three proteins can be better compared? Best regards. Yeping ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Marko Hyvonen Department of Biochemistry, University of Cambridge mh...@cam.ac.uk +44 (0)1223 766 044 @HyvonenGroup http://hyvonen.bioc.cam.ac.uk ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] APBS TOOLS 2.1 does not work
Dear all,
I am trying to use APBS TOOLs 2.1 to calculate electrostatic potential of
proteins. After I finish "set grid", I press the "set grid" button, I get the
following error,
(, ImportError('No module named pdb2pqr',),
)
In show error 2
Could you tell what is the cause of the error and how to fix it?
Best regards.___
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[PyMOL] "Qt not available" error from compilation with python2 but not python3
dear all, I am trying to compile pymol from source (https://github.com/schrodinger/pymol-open-source.git). Python 3 and python 2 both have been installed in my system. I first tried compile pymol with python 3 python3 setup.py install --prefix=~/pymol-install-py3 It can work. python3 setup.py install --prefix=~/pymol-install-py2 However, when I try to compile pymol with python2: python2 setup.py install --prefix=~/pymol-install-py2 lauching pymol gives the following error: Qt not available, using GLUT/Tk interface Traceback (most recent call last): File "__init__.py", line 65, in pymol.launch(args) File "/home/sunyp/pymol-install-py2/lib64/python2.7/site-packages/pymol/__init__.py", line 436, in launch _cmd.runpymol(_cmd._get_global_C_object(), block_input_hook) NotImplementedError: compile with --glut Even if I re-compile with --glut: python2 setup.py install --prefix=~/pymol-install-py2 the same error occurs. PyQt4 has been install in my system with yum install. I am very confused and wish to know why qt cannot be fould by pymol comoled with python2. Could you help me with that? Thank you in advacne. Yeping Sun ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to display electronic density for nucleic acid pymol
Dear Pymol users, I wish to prepare a image which looks like the picture at the follow link: https://drive.google.com/file/d/1HPwTCNqD7hlTPX9QDHif00YW5ZIv8PCa/view?usp=sharing I have ckecked the pymolwiki for different mode for drawing nucleic acid ladder and ring, but cannot find any thing that can produce an image like what I want. I don't know how to change the phosphoric acid backbond to stick from what looks like putty. Could you help me what this? I will be very grateful if you can help. Best regards. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to print the time stample on each frame of the movie for molecular dynamics trajectory in Pymol?
Dear All, I load a molecular dynamics (gromacs) trajectory into Pymol and wish to make a movie with it. The trajectory contains 2500 frames, corresponding to 200 ns simulation time, so each frame represents 80 ps. I wish to print time stample on each stample. For example, on the first frame, " 0 ns" is printed; on the second frame, "80 ps" is printed; on the third frame, "160 ps" is printed. How I cannot find any clue how to do this. Could you have any clue how to finish this task? Best regards, Yeping Sun___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to compile pymol with --glut?
Hi Thomas, Thank you and I know this has been asked before, but following the suggestion posted by you does not solve the problem. After run the two commands: rm -rf build python2 setup.py --glut install --prefix=~/pymol-install-py2 The same error still comes out. -- From:Thomas Holder Sent At:2020 Feb. 11 (Tue.) 17:34 To:孙业平 Cc:pymol-users Subject:Re: [PyMOL] How to compile pymol with --glut? Hi Yeping, This has been asked before (by you :-)), see here: https://sourceforge.net/p/pymol/mailman/message/36766620/ Cheers, Thomas > On Feb 8, 2020, at 2:12 PM, 孙业平 via PyMOL-users > wrote: > > Dear pymol users, > > I compiled pymol following the guide at > https://pymolwiki.org/index.php/Linux_Install in my CentOS 8 system. > When I tried to launch pymol by the "./pymol" command, I got the following > error: > > Qt not available, using GLUT/Tk interface > Traceback (most recent call last): > File > "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", > line 65, in > pymol.launch(args) > File > "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", > line 441, in launch > _cmd.runpymol(_cmd._get_global_C_object(), block_input_hook) > NotImplementedError: compile with --glut > > I then removed the "bin" and the "lib64" directories in the > "pymol-open-source-build" directory and recompiled pymol with the following > command: >python3 setup --glut install > --prefix=~/software/Pymol/pymol-open-source-build > > However, the newly generated pymol binary file does not work either. Launch > pymol give the same "Qt not available, using GLUT/Tk interface" error. > > Could you help me with this?Thank you in advance. > > Best regards. > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Fw: How to compile pymol with --glut?
Using yum of centos or apt of Ubuntu cannot install the latest version. -- From:Robi Gus Sent At:2020 Feb. 14 (Fri.) 22:00 To:孙业平 Subject:Re: [PyMOL] How to compile pymol with --glut? much easier to use apt to install open source pymol binaries Sent: Friday, February 14, 2020 at 7:47 AM From: "sunyeping via PyMOL-users" To: "Thomas Holder" Cc: pymol-users Subject: Re: [PyMOL] How to compile pymol with --glut? Hi Thomas, Thank you and I know this has been asked before, but following the suggestion posted by you does not solve the problem. After run the two commands: rm -rf build python2 setup.py --glut install --prefix=~/pymol-install-py2 The same error still comes out. -- From:Thomas Holder Sent At:2020 Feb. 11 (Tue.) 17:34 To:孙业平 Cc:pymol-users Subject:Re: [PyMOL] How to compile pymol with --glut? Hi Yeping, This has been asked before (by you :-)), see here: https://sourceforge.net/p/pymol/mailman/message/36766620/ Cheers, Thomas > On Feb 8, 2020, at 2:12 PM, 孙业平 via PyMOL-users > wrote: > > Dear pymol users, > > I compiled pymol following the guide at > https://pymolwiki.org/index.php/Linux_Install in my CentOS 8 system. > When I tried to launch pymol by the "./pymol" command, I got the following > error: > > Qt not available, using GLUT/Tk interface > Traceback (most recent call last): > File > "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", > line 65, in > pymol.launch(args) > File > "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", > line 441, in launch > _cmd.runpymol(_cmd._get_global_C_object(), block_input_hook) > NotImplementedError: compile with --glut > > I then removed the "bin" and the "lib64" directories in the > "pymol-open-source-build" directory and recompiled pymol with the following > command: >python3 setup --glut install > --prefix=~/software/Pymol/pymol-open-source-build > > However, the newly generated pymol binary file does not work either. Launch > pymol give the same "Qt not available, using GLUT/Tk interface" error. > > Could you help me with this?Thank you in advance. > > Best regards. > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Effect of different align method
Dear pymol users, I am trying to align two very similar trimeric molecules. I tried different alignment commands including "align", "cealign" and "super", but none of them gives satisfying effect. Athough the backbone conformations and orientations of two two molecules look very similar, there are obvious displacements between them after alignment with these three commands. The rmsd of the two molecules for these three methods are 2.250, 4.682, 2.206 and 2.206, respectively. I wonder whether there is any better alignment command or there are any parameters that can be passed to these three alignment commands to improve the effects. Could you help me check this? The pdb files of these two molecules, the image for the two molecules after using "super" command, and the alignment effect in the publication I mentioned can be found at the following link. https://drive.google.com/file/d/1ff3XgTexgdul-SezUz75dVoCx2cL5YPL/view?usp=sharing With many thanks. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Effect of different align method
Hello Julien Cappèle, Thank you for your response. I didn't mean to keep the input file in secrete. I have changed the access right to them, so you can download them freely. Best, Yeping Sun -- From:Julien CAPPELE Sent At:2020 Jun. 17 (Wed.) 17:05 To:孙业平 Subject:Re: [PyMOL] Effect of different align method Hello Sunyeping, I would suggest you to try TM-align, and a very good way to use it for multi-protein alignment is to use their server mTM-align. TM-align is a very robust alignment tool that will in most of the case, give you a better structural based alignment with low to zero input from the sequence. https://yanglab.nankai.edu.cn/mTM-align/ Also, if you are not working on secret stuff, you can give me access so I can rework the output files from mTM-align server to give you a RMSD-colored alignment in PyMOL. On PyMOL only, I didn't try to implement TM-align because I use Windows, but the developers said that a linux implementation could be possible if you are a bit familiar with compiling softwares. - Julien Cappèle Doctorant - 2ème année - ED C2MP Université de Lorraine CRM² - UMR CNRS 7036 julien.capp...@univ-lorraine.fr Tel: (+33)6 99 18 59 03 - Le mer. 17 juin 2020 à 05:06, sunyeping via PyMOL-users a écrit : Dear pymol users, I am trying to align two very similar trimeric molecules. I tried different alignment commands including "align", "cealign" and "super", but none of them gives satisfying effect. Athough the backbone conformations and orientations of two two molecules look very similar, there are obvious displacements between them after alignment with these three commands. The rmsd of the two molecules for these three methods are 2.250, 4.682, 2.206 and 2.206, respectively. I wonder whether there is any better alignment command or there are any parameters that can be passed to these three alignment commands to improve the effects. Could you help me check this? The pdb files of these two molecules, the image for the two molecules after using "super" command, and the alignment effect in the publication I mentioned can be found at the following link. https://drive.google.com/file/d/1ff3XgTexgdul-SezUz75dVoCx2cL5YPL/view?usp=sharing With many thanks. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to select s series of residues that contain the selected atom
Dear pymol user, I select a series of atoms with the follow command in pymol: select atoms, chian A within 4 of chain B I wonder how to select the resides containing the selected "atoms", and how to return the names and indexes of these residues. Thank you in advance! Best regards, Yeping Sun___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] present b factor putty on select
Dear all, I know that if you want to visualize b facotor of a objector in pymol, you can use A>Present>b factor putty. However, how can show the b factor putty on a certain selection of the object? Is there any command line to do this or do I have to create a new object for the selection and still use the A>Present>b factor putty operation? Thank you, Best regards___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] [EXTERNAL] present b factor putty on select
Hi, Blaine,
Thank you, that's helpful. But a problem with creating a new object is that the
conformation of the newly created object for the selection is sightly different
from its counterpart in the original object. If the original object is shown as
cartoon, then both the putty presentation of new object and the cartoon
presentation of its counterpart in the original object at site of the
conformational difference will appear in the image produced in this way, and
that's ugly. Is there a way the avoid this shortcoming?
Best,
--
From:Mooers, Blaine H.M. (HSC)
Sent At:2020 Oct. 27 (Tue.) 18:09
To:孙业平 ; pymol-users
Subject:RE: [PyMOL] [EXTERNAL] present b factor putty on select
I am sorry. I am wrong. I should have tested by suggestion.
Irregardless of the selection that I specify, the entire chain is changed.
I would go with your plan B and create a new object for the selection.
create test, resi 100:150
preset.b_factor_putty("test")
The above worked with pdb file 4dgr.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
From: Mooers, Blaine H.M. (HSC) [blaine-moo...@ouhsc.edu]
Sent: Tuesday, October 27, 2020 4:54 AM
To: sunyeping; pymol-users
Subject: Re: [PyMOL] [EXTERNAL] present b factor putty on select
Hi sunyeping,
You are right; there is a way via the command line:
preset.b_factor_putty(selection='all')
Replace "all" with your selection.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
____
From: sunyeping via PyMOL-users [pymol-users@lists.sourceforge.net]
Sent: Tuesday, October 27, 2020 3:09 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] present b factor putty on select
Dear all,
I know that if you want to visualize b facotor of a objector in pymol, you can
use A>Present>b factor putty. However, how can show the b factor putty on a
certain selection of the object? Is there any command line to do this or do I
have to create a new object for the selection and still use the A>Present>b
factor putty operation?
Thank you,
Best regards
___
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[PyMOL] Dose the thickness of residues reflect b-factor in cartoon putty representation?
Dear all, When you use "cartoon putty[, selection]" command in pymol, you will get the cartoon putty representation of your selection. And the backbond of the selection show different thickness. So dose the thickness of residues reflect b-factor in cartoon putty representation? Best regards Yeping Sun___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to label residue name on top of sphere representation
Dear all, I wish to label residue name on top of sphere representation, but I find it is difficult. I tried the following command select sele, c. A & resi 47 & name CB show sphere, c. A & resi 47 lable sele, "Y47" I and the "Y47" label is hidden inside the sphere and cannot be seen. Even if I set the sphere to be 80 % transparency, the label cannot be seen yet. So what the the correct way to make such a labelling? Best regards, Yeping Sun___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] pymol installation error
Dear pymol users, I am installing pymol in Centos 7 according to the guide in https://pymolwiki.org/index.php/Linux_Install. I encounter an error of "error: command 'g++' failed with exit status 1". A fill output of the install command is as following: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/Scene.cpp -o build/temp.linux-x86_64-3.7/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/SceneView.cpp -o build/temp.linux-x86_64-3.7/layer1/SceneView.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer4/Cmd.cpp -o build/temp.linux-x86_64-3.7/layer4/Cmd.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory #include ^ compilation terminated. layer1/Scene.cpp: In function ‘void SceneOriginSet(PyMOLGlobals*, const float*, int)’: layer1/Scene.cpp:2557:42: error: no matching function for call to ‘make_vec3(glm::vec3&)’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ layer1/Scene.cpp:2557:42: note: candidate is: In file included from /usr/include/glm/gtc/type_ptr.hpp:178:0, from layer1/Ray.h:23, from layer1/View.h:23, from layer1/PyMOLObject.h:28, from layer1/Scene.cpp:32: /usr/include/glm/gtc/type_ptr.inl:336:40: note: template glm::tvec3 glm::make_vec3(const T*) GLM_FUNC_QUALIFIER tvec3 make_vec3(T const * const ptr) ^ /usr/include/glm/gtc/type_ptr.inl:336:40: note: template argument deduction/substitution failed: layer1/Scene.cpp:2557:42: note: mismatched types ‘const T*’ and ‘glm::tvec3’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ error: command 'g++' failed with exit status 1 Would you be kind to help me figure out what's wrong with I installation? I will appreciate much of any help. Best regards.___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] pymol installation error
Dear all, Now I revised Line 4 in the SceneView.cpp file from "#include " to "#include ". The error "layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory" disappeared, but a now error appeared: layer1/SceneView.cpp:31:55: error: no matching function for call to ‘equal(const vec3&, const vec3&, float)’ Do you know how to deal with such an eorror? With many thanks! Best regards -- From:pymol-users Send Time:2021年9月12日(星期日) 15:39 To:pymol-users Subject:[PyMOL] pymol installation error Dear pymol users, I am installing pymol in Centos 7 according to the guide in https://pymolwiki.org/index.php/Linux_Install. I encounter an error of "error: command 'g++' failed with exit status 1". A fill output of the install command is as following: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/Scene.cpp -o build/temp.linux-x86_64-3.7/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/SceneView.cpp -o build/temp.linux-x86_64-3.7/layer1/SceneView.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer4/Cmd.cpp -o build/temp.linux-x86_64-3.7/layer4/Cmd.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory #include ^ compilation terminated. layer1/Scene.cpp: In function ‘void SceneOriginSet(PyMOLGlobals*, const float*, int)’: layer1/Scene.cpp:2557:42: error: no matching function for call to ‘make_vec3(glm::vec3&)’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ layer1/Scene.cpp:2557:42: note: candidate is: In file included from /usr/include/glm/gtc/type_ptr.hpp:178:0, from layer1/Ray.h:23, from layer1/View.h:23, from layer1/PyMOLObject.h:28, from layer1/Scene.cpp:32: /usr/include/glm/gtc/type_ptr.inl:336:40: note: template glm::tvec3 glm::make_vec3(const T*) GLM_FUNC_QUALIFIER tvec3 make_vec3(T const * const ptr) ^ /usr/include/glm/gtc/type_ptr.inl:336:40: note: template argument deduction/substitution failed: layer1/Scene.cpp:2557:42: note: mismatched types ‘const T*’ and ‘glm::tvec3’ I->m_view.translate(glm::make_vec3(v1)); /* offset view to compensate */ ^ error: command 'g++' failed with exit status 1 Would you be kind to help me figure out what's wrong with I installation? I will appreciate much
Re: [PyMOL] pymol installation error
Dear Mr. Jarrett, Yes, with the glm of version 0.0.9, pymol can be installed successful. Thank you very much:) -- From:Jarrett Johnson Send Time:2021年9月13日(星期一) 01:30 To:孙业平 Cc:pymol-users Subject:Re: [PyMOL] pymol installation error Hello, Looks like the glm version that you're currently using (I'm assuming 0.9.6--default package for Centos 7) is not up to date with the ones we're currently using (0.9.9). The location for glm headers within their library have changed a bit since the last several years. I might have to think of a way to reconcile these issues sometime this week. In the meantime if you'd like, I suggest picking up the latest package from https://github.com/g-truc/glm; alternatively, currently stick with your version and include and use `glm::epsilonEqual` over `glm::equal` on lines 31 and 32 of that source file. Hope that helps, Jarrett J On Sun, Sep 12, 2021 at 4:41 AM sunyeping via PyMOL-users wrote: Dear all, Now I revised Line 4 in the SceneView.cpp file from "#include " to "#include ". The error "layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory" disappeared, but a now error appeared: layer1/SceneView.cpp:31:55: error: no matching function for call to ‘equal(const vec3&, const vec3&, float)’ Do you know how to deal with such an eorror? With many thanks! Best regards -- From:pymol-users Send Time:2021年9月12日(星期日) 15:39 To:pymol-users Subject:[PyMOL] pymol installation error Dear pymol users, I am installing pymol in Centos 7 according to the guide in https://pymolwiki.org/index.php/Linux_Install. I encounter an error of "error: command 'g++' failed with exit status 1". A fill output of the install command is as following: running build running build_py running build_ext building 'pymol._cmd' extension g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/Scene.cpp -o build/temp.linux-x86_64-3.7/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer1/SceneView.cpp -o build/temp.linux-x86_64-3.7/layer1/SceneView.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp g++ -pthread -B /home/sunyp/software/anaconda/build/compiler_compat -Wl,--sysroot=/ -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/home/sunyp/software/anaconda/build/lib/python3.7/site-packages/numpy/core/include -I/home/sunyp/software/anaconda/build/include -I/home/sunyp/software/anaconda/build/include/freetype2 -I/home/sunyp/software/anaconda/build/include/libxml2 -I/home/sunyp/software/anaconda/build/include/python3.7m -c -MMD layer4/Cmd.cpp -o build/temp.linux-x86_64-3.7/layer4/Cmd.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer1/SceneView.cpp:4:41: fatal error: glm/ext/vector_relational.hpp: No such file or directory #include ^ compilation terminated. layer1/Scene.cpp: In function ‘void SceneOriginSet(PyMOLGlobals*, const float*, int)’: layer1/Scene.cpp:2557:42: e
[PyMOL] How to import anaconda packages in Pymol?
Dear all, I installed Pymol in CentOS from source following the guide in "https://pymolwiki.org/index.php/Linux_Install";. I compiled Pymol with the Python from anaconda, but I found that I cannot import anaconda packages (such as pandas, numpy, etc.) in Pymol. The "import pandas" command will return "no such module named pandas" error. Could yuo tell me how to let pymol use the anaconda packages? I will appreciate any help. Best regards ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to label on surface
Dear Pymol users, I wish to label the one-letter residue names for a bunch of selected resides on surface representation of a protein, but I found the labels cannot be seen on the image. It seems that these labels can been seen on cartoon representation when the surface is hide. Could you tell to how to show the labels on the surface? I will appreciate any help! Best regards___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to label atom at proper positions?
Dear pymol users, I select a series of CA atoms in a structure in pymol and show them as sphere in pymol and want to label them. If using the label menu at the up-right conner of pymol, the labels shown overlaps with spheres and can not be seen. So I wish to show the labels at a bit distance from the seleccted atoms. Is there a method to do that? I will appreciate to any help! Best regards ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to label atom at proper positions?
Dear Professor Halil İbrahim Özdemir, Thank you for your help. The labels shown now are fomatted as "(THR339)", "(SER308)", etc. I wonder how to show them as single-letter codes plus the numbers without the parentheses, like "T339", "S308". Thank you again. Best, -- From:Halil İbrahim Özdemir Send Time:2022年1月18日(星期二) 18:50 To:孙业平 Subject:Re: [PyMOL] How to label atom at proper positions? Hi Sunyeping, You can easily apply the following script from PyMOL terminal. Have a nice days. # Select all C-Alpha atoms and set the object name as "CAs" select CAs, n. CA # Give Label Them as (Residue Name+Residue Number) label CAs, "(%s%s)" % (resn, resi) # Set Label Positions for object "CAs" set label_position, (3,2,1), CAs Regards, sunyeping via PyMOL-users , 18 Oca 2022 Sal, 13:14 tarihinde şunu yazdı: Dear pymol users, I select a series of CA atoms in a structure in pymol and show them as sphere in pymol and want to label them. If using the label menu at the up-right conner of pymol, the labels shown overlaps with spheres and can not be seen. So I wish to show the labels at a bit distance from the seleccted atoms. Is there a method to do that? I will appreciate to any help! Best regards ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to label atom at proper positions?
Hello professor,
Now I have a new question: how to label the selected CA atoms with strings
representing mutations, like "T123D", "K339R", etc?
I tried to use these commands:
select CAs, resi 123+339
mut = ["T123D", "K139R", "G223S", "M321S"]
label CAs, mut.pop
but I found that the labels are put in the wrong positions. So what is the
correct way the show the labels for mutations?
Best regards
--
From:Halil İbrahim Özdemir
Send Time:2022年1月19日(星期三) 14:05
To:孙业平
Subject:Re: [PyMOL] How to label atom at proper positions?
You can modify the previous script like this,
# ONE LETTER CODES
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',\
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',\
'GLY':'G', 'PRO':'P', 'CYS':'C'}
# Select all C-Alpha atoms and set the object name as "CAs"
select CAs, n. CA
# Give Label Them as (Residue Name+Residue Number)
label CAs, "%s%s" % (one_letter[resn],resi)
# Set Label Positions for object "CAs"
set label_position, (3,2,1), CAs
Regards,
sunyeping , 19 Oca 2022 Çar, 06:43 tarihinde şunu yazdı:
Dear Professor Halil İbrahim Özdemir,
Thank you for your help. The labels shown now are fomatted as "(THR339)",
"(SER308)", etc.
I wonder how to show them as single-letter codes plus the numbers without the
parentheses, like "T339", "S308".
Thank you again.
Best,
------
From:Halil İbrahim Özdemir
Send Time:2022年1月18日(星期二) 18:50
To:孙业平
Subject:Re: [PyMOL] How to label atom at proper positions?
Hi Sunyeping,
You can easily apply the following script from PyMOL terminal. Have a nice days.
# Select all C-Alpha atoms and set the object name as "CAs"
select CAs, n. CA
# Give Label Them as (Residue Name+Residue Number)
label CAs, "(%s%s)" % (resn, resi)
# Set Label Positions for object "CAs"
set label_position, (3,2,1), CAs
Regards,
sunyeping via PyMOL-users , 18 Oca 2022 Sal,
13:14 tarihinde şunu yazdı:
Dear pymol users,
I select a series of CA atoms in a structure in pymol and show them as sphere
in pymol and want to label them. If using the label menu at the up-right conner
of pymol, the labels shown overlaps with spheres and can not be seen. So I wish
to show the labels at a bit distance from the seleccted atoms. Is there a
method to do that? I will appreciate to any help!
Best regards
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[PyMOL] why does coordinates not overlap with map
Dear pymol users, I have a coordinate file (pdb) and a map file (mtz), and I want to make a image that shows both the coordinate and the map. I generate a .map.ccp4 file using fft in CCP4 program. However, when I open the pdb file and the .map.ccp4 in pymol, I find the coordinates are out of the map. Please see the image at the following link: https://drive.google.com/file/d/1TmH-mFCnsCNghcq4RQJ9mNOBlTfCRsHW/view?usp=sharing Could anyone tell me how to map them overlap? Thank you in advance. Best regards___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to use cmd.label command
Dear all,
I want to label residues with the resn+resi, and I tried the following command
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',\
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',\
'GLY':'G', 'PRO':'P', 'CYS':'C'}
select CAs, obj & n. CAs
label CAs, "%s%s" % (one_letter[resn],resi)
These work find. However, when I write these in a script and the last two
commands are written as:
cmd.select('CAs', 'obj & n. CAs')
cmd.label('CAs', "%s%s" % (one_letter[resn],resi))
it gives the following error:
NameError: name 'resn' is not defined
So could anyone tell me how to correctly use the cmd.label command?
Thank you very much in advance
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[PyMOL] how to use cmd.label command
Dear all,
I want to label residues with the resn+resi, and I tried the following command
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',\
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',\
'GLY':'G', 'PRO':'P', 'CYS':'C'}
select CAs, obj & n. CAs
label CAs, "%s%s" % (one_letter[resn],resi)
These work find. However, when I write these in a script and the last two
commands are written as:
cmd.select('CAs', 'obj & n. CAs')
cmd.label('CAs', "%s%s" % (one_letter[resn],resi))
it gives the following error:
NameError: name 'resn' is not defined
So could anyone tell me how to correctly use the cmd.label command?
Thank you very much in advance
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