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[PyMOL] color by index
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From: Chen, Q. <qi...@pi...> - 2020-06-18 13:21:01
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Will spectrum just works for your purpose? spectrum count, blue red, yourprotein, byres=1 you can switch off byres if you really want color by atom index. Charles > hello everyone! > I am trying to color an explicit distribution by color (say blue to red) > pls help me with the command color by index > On Jun 18, 2020, at 12:20 AM, pym...@li... wrote: > > Send PyMOL-users mailing list submissions to > pym...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fpymol-users&data=02%7C01%7Cqic8%40pitt.edu%7Ce118586bf6ff40e8fb8508d8133ee536%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637280508154218214&sdata=wvtOxRB5m%2Bg7ASumbPcJ%2BB%2BtJzO92NpCWEvtHb7bxsI%3D&reserved=0 > or, via email, send a message with subject or body 'help' to > pym...@li... > > You can reach the person managing the list at > pym...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of PyMOL-users digest..." > > > Today's Topics: > > 1. Re: Effect of different align method (Robert Campbell) > 2. Color by index (Vertika Gautam) > 3. help (Vertika Gautam) > 4. help (Vertika Gautam) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 17 Jun 2020 16:49:52 -0400 > From: Robert Campbell <rob...@qu...> > To: pym...@li... > Subject: Re: [PyMOL] Effect of different align method > Message-ID: <202...@ad...> > Content-Type: text/plain; charset=UTF-8 > > Hello Sunyeping, > > I would first point out that if you align on chain A of each molecule, then chain B of ASFV aligns with chain C of MTUB and vice versa. In other words you don't have the same assignment of chain ids in your trimer. The alignment of just alpha carbons of chain A with "align" gives an RMSD of 1.78 ? for 81 atoms and for "super" gives an RMSD of 1.746 ? for 81 atoms. That may be the best that you can do, but if you want to align the whole trimer than you need to rename chain B to chain C and chain C to chain B for one of your molecules. > > You can do that renaming within PyMOL with these commands: > > PyMOL>alter MTUB_trimer & c. B, chain="D" > PyMOL>alter MTUB_trimer & c. C, chain="B" > PyMOL>alter MTUB_trimer & c. D, chain="C" > > (I'm just using "D" as an intermediate name here) > > If you do that, then aligning all alpha carbons gives an RMSD of 2.189 ? for "align" and 1.845 ? for "super". > > Cheers, > Rob > > On Wed, 2020-06-17 21:04 +0800, sunyeping via PyMOL-users <pym...@li...> wrote: > >> Hello Julien Capp?le, >> 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 <jul...@un...> >> Sent At:2020 Jun. 17 (Wed.) 17:05 >> To:??? <sun...@al...> >> 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://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fyanglab.nankai.edu.cn%2FmTM-align%2F&data=02%7C01%7Cqic8%40pitt.edu%7Ce118586bf6ff40e8fb8508d8133ee536%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637280508154218214&sdata=isejknGXC9BfuPHsGXhYBsux0pWwNIBGuiZntSyR2BY%3D&reserved=0 >> >> 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 Capp?le >> Doctorant - 2?me ann?e - ED C2MP >> Universit? de Lorraine >> CRM? - UMR CNRS 7036 >> jul...@un... >> Tel: (+33)6 99 18 59 03 >> --------------------------------------------- >> >> Le mer. 17 juin 2020 ? 05:06, sunyeping via PyMOL-users >> <pym...@li...> a ?crit : 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://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1ff3XgTexgdul-SezUz75dVoCx2cL5YPL%2Fview%3Fusp%3Dsharing&data=02%7C01%7Cqic8%40pitt.edu%7Ce118586bf6ff40e8fb8508d8133ee536%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637280508154218214&sdata=dCFxgp3VTqywcrbc5b3ID4VcKcMMvOBKqqB2oXrwrTE%3D&reserved=0 >> >> With many thanks. >> >> _______________________________________________ >> PyMOL-users mailing list >> Archives: >> https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&data=02%7C01%7Cqic8%40pitt.edu%7Ce118586bf6ff40e8fb8508d8133ee536%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637280508154218214&sdata=nldC9GskvF2yZFhsem7WE%2Fw5zp%2BYen9p0Rb8LBfrdEU%3D&reserved=0 >> Unsubscribe: >> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&data=02%7C01%7Cqic8%40pitt.edu%7Ce118586bf6ff40e8fb8508d8133ee536%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637280508154218214&sdata=%2Bx7ToQjAdGcCO%2BLYE538mCL8nA%2FDzrj%2FMIAejis7jYo%3D&reserved=0 >> > > > > -- > Robert L. Campbell, Ph.D. > Academic Advisor, BHSc Program > Assistant Professor, Dept. of Biomedical & Molecular Sciences, > Queen's University, Kingston, ON K7L 3N6 Canada > Botterell Hall Rm 644 Tel: 613-533-6821 > <rob...@qu...> https://nam05.safelinks.protection.outlook.com/?url=http:%2F%2Fpldserver1.biochem.queensu.ca%2F~rlc&data=02%7C01%7Cqic8%40pitt.edu%7Ce118586bf6ff40e8fb8508d8133ee536%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637280508154218214&sdata=FDbdIfTMBWfhWcD6HBL3EDIlexLk84hM8qQwypQRu18%3D&reserved=0 > > > > ------------------------------ > > Message: 2 > Date: Thu, 18 Jun 2020 12:05:06 +0800 > From: Vertika Gautam <var...@gm...> > To: pym...@li... > Subject: [PyMOL] Color by index > Message-ID: > <CAD...@ma...> > Content-Type: text/plain; charset="utf-8" > > hello everyone! > I am trying to color an explicit distribution by color (say blue to red) > pls help me with the command color by index > > > thanks! > Vertika Gautam > > Research Assistant > Drug Design and Development Research Group (DDDRG) > Department of Chemistry, Faculty of Science > University of Malaya > > > > *e-mail address: var...@gm... > <var...@gm...> > var...@ho... <var...@ho...> > 01112294191* > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 3 > Date: Thu, 18 Jun 2020 12:08:45 +0800 > From: Vertika Gautam <var...@gm...> > To: pym...@li... > Subject: [PyMOL] help > Message-ID: > <CAD2fjZe=FPV...@ma...> > Content-Type: text/plain; charset="utf-8" > > hello everyone! > I am trying to color an explicit distribution by color (say blue to red) > pls help me with the command color by index > > > thanks! > > -- > Vertika Gautam > > Research Assistant > Drug Design and Development Research Group (DDDRG) > Department of Chemistry, Faculty of Science > University of Malaya > > > > *e-mail address: var...@gm... > <var...@gm...> > var...@ho... <var...@ho...> > 01112294191* > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 4 > Date: Thu, 18 Jun 2020 12:19:15 +0800 > From: Vertika Gautam <var...@gm...> > To: pym...@li... > Subject: [PyMOL] help > Message-ID: > <CAD2fjZdt6x3E=JYQrcfwhddMYkGDkTqfEwyD9Kni=u6v...@ma...> > Content-Type: text/plain; charset="utf-8" > > Hello everyone > > I am trying to make a figure showing the potential surface and binding > pocket as shown in the attached figure. Can anyone help me with the > commands? > Thanks in advance for your help! > [image: image.png] > -- > Vertika Gautam > > Research Assistant > Drug Design and Development Research Group (DDDRG) > Department of Chemistry, Faculty of Science > University of Malaya > > > > *e-mail address: var...@gm... > <var...@gm...> > var...@ho... <var...@ho...> > 01112294191* > -------------- next part -------------- > An HTML attachment was scrubbed... > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image.png > Type: image/png > Size: 115742 bytes > Desc: not available > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: sample_image.jpg > Type: image/jpeg > Size: 14732 bytes > Desc: not available > > ------------------------------ > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fpymol-users&data=02%7C01%7Cqic8%40pitt.edu%7Ce118586bf6ff40e8fb8508d8133ee536%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637280508154218214&sdata=wvtOxRB5m%2Bg7ASumbPcJ%2BB%2BtJzO92NpCWEvtHb7bxsI%3D&reserved=0 > Unsubscribe: https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&data=02%7C01%7Cqic8%40pitt.edu%7Ce118586bf6ff40e8fb8508d8133ee536%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637280508154228212&sdata=7sq0fZeqxJ7PfE%2FNccS3GNxm2JLXvd8M1KKmjVJf8lE%3D&reserved=0 > > ------------------------------ > > End of PyMOL-users Digest, Vol 169, Issue 32 > ******************************************** |
