Re: [PyMOL] RMS over a MD trajectory.
Oh, I see... It looks like I'll need to end up writing a short script that does the loop along the trajectory together with a correct RMS calculation. Thanks for the tip, Carsten. Cheers, Albert On 05/08/2015 04:11 PM, Schubert, Carsten [JRDUS] wrote: Hi Al, based on my experience running align or super with cycles=0 has the tendency to produce inferior alignment results. So depending on how similar the conformation of your structures are you may end up with skewed statistics. What I've done in the past and for a paper I'm working on now is to run the alignment with default parameters to get the best superposition and then calculate the statistics by hand from the superposed structures. Not sure if cmd.rms() would do this for all residues w/o outlier rejection, so I ended up writing code for myself. The colorbyrmsd.py (http://pymolwiki.org/index.php/ColorByRMSD) script gives a nice illustration on how to approach this this. Carsten -Original Message- From: Albert Solernou [mailto:a.soler...@leeds.ac.uk] Sent: Friday, May 08, 2015 10:04 AM To: Thomas Holder Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] RMS over a MD trajectory. Thanks Thomas, I was already printing k[i][3] (RMSD before refinement) instead of k[i][0] (RMSD after refinement) but your cycles=0 looks cleaner. Cheers, Albert On 05/06/2015 05:14 PM, Thomas Holder wrote: Hi Albert, Please pay attention to the difference between all-atom RMSD and RMSD after outlier rejection. http://pymolwiki.org/index.php/Align#RMSD If your trj and pdb1 have identical topology and matching atom identifiers, then you can also use cmd.rms(). http://pymolwiki.org/index.php/Rms Cheers, Thomas On 06 May 2015, at 11:56, Albert Solernou a.soler...@leeds.ac.uk wrote: Terribly useful Carsten! I could easily do a loop and get the RMS along the trajectory: k = [] for i in range(1,101): k.append(cmd.align(trj,pdb1,mobile_state=i)) for i in range(100): print k[i][0] Cheers, Albert On 05/06/2015 04:20 PM, Schubert, Carsten [JRDUS] wrote: Hi Al, you would need to go through the Python API: python rms=cmd.align(mobCA,tarCA, quiet=0) print rms python end rms contains a tuple with various parameters related to the superposition. The first value in the tuple i.e. rms[0] should be the RMS value. HTH Carsten -Original Message- From: Albert Solernou [mailto:a.soler...@leeds.ac.uk] Sent: Wednesday, May 06, 2015 8:32 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] RMS over a MD trajectory. Hi, I am trying to compute the RMS between a PDB file and a Gromacs trajectory. I can see that align does things correctly when: align trj, pdb1, mobile_state=1 i. e., when I align the first snapshot of the trajectory with the PDB file. I also understand that PyMOL does compute the RMS along the trajectory if I simply: align trj, pdb1 as it is told in: http://www.pymolwiki.org/index.php/Align However, I am unable to get the list of RMS values printed out. How could I do that? Thanks, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- 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 -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- 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:
[PyMOL] How to Highlight B-Values of Side Chains?
Hello: I am trying to see the effect of side-chain fluctuation on molecular permeation through a transmembrane protein channel. The idea is create a pdb file with a column of B-values related to the RMSF values of the MD trajectory. What I tried was to set the B-values of all heavy atom main-chain atoms to 1.0. Then all the B side-chain values were set equal to the RMSF value from the trajectory, using the correct formula relating RMSF fluctuation to B-value. But, the above method blows up in pymol when trying to use the Action --- Preset --- b factor putty option. I think this is probably due to the fact that all main-chain atoms are equal to 1, and the algorithm cannot handle this. Can someone please provide me with a way to clearly see the fluctuation of sid-chain atoms in the present of the main-chain atoms? Thanks so much. Regards, Angelo -- 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 connect to atoms?
Dear pymol users I have one pdb file containing two peptides. Based on experimental data, I should connect two peptides to obtain one new peptide in pdb file. This connection is as follows: CD atom of GLU residue from peptide 1 and NZ atom of LYS residue from peptide 2. How to make this connection using pymol without any change in the format of pdb file (after saving this file)? I want to use this new pdb file as an input file in gromacs package. Any help will highly appreciated. -- 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
Re: [PyMOL] how to connect to atoms?
Hi Leila, This too is more a question for the Gromacs mailing list. Gromacs does not read bond information (CONECT records) from a PDB file. It only reads the ATOM/HETATM records and sets bonds based on the force field building block definitions and the special bonds (such as the isopeptide link) in the specbond.dat file. Cheers, Tsjerk On Mon, May 11, 2015 at 10:02 PM, leila karami karami.lei...@gmail.com wrote: You are right. I will ask my question gromacs mailing list. But, please answer my first question. I create a covalent bond between these 2 atoms using hyperchem. After I saved new pdb file, the format of pdb file was changed. Which software or model builder is appropriate for this goal? Thanks in advance. --- *Dr. Leila KaramiPostdoctoral ResearcherInstitute of Biochemistry and BiophysicsUniversity of TehranTehran, Iran* *Email: karami.le...@ut.ac.ir karami.le...@ut.ac.ir karami.le...@ut.ac.ir* *Tel: +98 9193155894 %2B98%209193155894* On Tue, May 12, 2015 at 12:27 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Leila, Please ask this question on the gromacs mailing list. But first search the gromacs archives to see what's already there (which is most of what you ask). Cheers, Tsjerk On Mon, May 11, 2015 at 9:54 PM, leila karami karami.lei...@gmail.com wrote: Dear Tsjerk Thanks for your quick answer. Yes, the peptides are already positioned correctly. Which option in pdb2gmx does make this bond between two residues from two different chains? I want to make covalent bond between two atoms (CD atom of GLU residue from peptide 1 and NZ atom of LYS residue from peptide 2). What you mentioned is related to merging of two chains. I am beginner in this field. Please guide about that. -- Tsjerk A. Wassenaar, Ph.D. -- Tsjerk A. Wassenaar, Ph.D. -- 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
Re: [PyMOL] How to Highlight B-Values of Side Chains?
Hi Angelo, As far as I understand the putty representation takes the values from the b-factor of the Ca atom. Probably you should store your fluctuation values either on the Ca (leaving all the others atoms with 0.0 or any other value) or just set the same b-factor for all the atoms of a given residue. Either way you should get what you want. I think the error you are getting is because all the Ca have the same b-factor value is your error something like invalid putty settings (division by zero)? If you want all the Ca having the same b-factor and use the putty representation anyway you should do the following: set cartoon_putty_transform, 2 Cheers, Osvaldo. On Mon, May 11, 2015 at 6:35 PM, Angelo Rossi angelo.raymond.ro...@gmail.com wrote: Hello: I am trying to see the effect of side-chain fluctuation on molecular permeation through a transmembrane protein channel. The idea is create a pdb file with a column of B-values related to the RMSF values of the MD trajectory. What I tried was to set the B-values of all heavy atom main-chain atoms to 1.0. Then all the B side-chain values were set equal to the RMSF value from the trajectory, using the correct formula relating RMSF fluctuation to B-value. But, the above method blows up in pymol when trying to use the Action --- Preset --- b factor putty option. I think this is probably due to the fact that all main-chain atoms are equal to 1, and the algorithm cannot handle this. Can someone please provide me with a way to clearly see the fluctuation of sid-chain atoms in the present of the main-chain atoms? Thanks so much. Regards, Angelo -- 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 -- 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
