Re: [PyMOL] representing missing residues in pymol

Dear Steinberg Thank you very much for the idea Best Regards Priyan On Thu, Sep 25, 2014 at 7:33 PM, H. Adam Steinberg < h.adam.steinb...@gmail.com> wrote: > This is not as simple as you would like but PyMOL does have the ability to > manually build in missing atoms. And this feature allows you

Re: [PyMOL] selecting all instead of just one aa

I see. Great help, Thank you. Regards, Vaheh 8-5851 From: Matthew Baumgartner [mailto:mp...@pitt.edu] Sent: Thursday, September 25, 2014 3:01 PM To: Oganesyan, Vaheh; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] selecting all instead of just one aa In the bottom right it says 'Selec

Re: [PyMOL] selecting all instead of just one aa

In the bottom right it says 'Selecting Residues'. If you click on that it will cycle through the other selection levels. Matt On 09/25/2014 02:25 PM, Oganesyan, Vaheh wrote: Thanks, really easy, feel very special. By not choosing Mouse>Selection Mode>Chains how else one gets into that mode?

Re: [PyMOL] selecting all instead of just one aa

Thanks, really easy, feel very special. By not choosing Mouse>Selection Mode>Chains how else one gets into that mode? Just curious. Regards, Vaheh 8-5851 From: Matthew Baumgartner [mailto:mp...@pitt.edu] Sent: Thursday, September 25, 2014 2:19 PM To: pymol-users@lists.sourceforge.net Subject:

Re: [PyMOL] selecting all instead of just one aa

Hi, Go to the Mouse Menu > Selection Mode > Residues Matt Baumgartner On 09/25/2014 01:48 PM, Oganesyan, Vaheh wrote: All, During my PyMOL session I’ve “accidentally” entered into a mode when by clicking one amino acid whole chain becomes selected. How can I turn it off? It is a quite elabo

[PyMOL] selecting all instead of just one aa

All, During my PyMOL session I've "accidentally" entered into a mode when by clicking one amino acid whole chain becomes selected. How can I turn it off? It is a quite elaborate scene to start it over. Thank you for help. Regards, Vaheh Oganesyan MedImmune, ADPE www.medimmune.com To the exten

Re: [PyMOL] AutoDock Vina Plugin

Matt thanks for the response. I did try both of those things you suggested. I am using a windows based system, but it is in the directory. I even tried uninstalling it and then re-installing to see if that would fix it. I have also rebooted the computer. I was hoping it was something simple tha

Re: [PyMOL] AutoDock Vina Plugin

Hi, Did you try restarting pymol? Also, check your startup directory to see if it was moved there. On unix, it's ~/.pymol/startup/ you should see the autodock.py script there. HTH, Matt On 09/25/2014 11:56 AM, Joseph Brown wrote: I am trying to install the autodock vina plugin for PyMOL. I

[PyMOL] AutoDock Vina Plugin

I am trying to install the autodock vina plugin for PyMOL. I go to the plugin tab, manage plugins, install and get a message that it installed but it does not appear under the Plugin tab. If I go to remove it is showing up as being installed. Any suggestions would be helpful. -Joe

Re: [PyMOL] representing missing residues in pymol

This is not as simple as you would like but PyMOL does have the ability to manually build in missing atoms. And this feature allows you to manually fill in missing sequences. I have used it many times to make a specific point, noting that the missing AAs were manually added to the figure. On Se

Re: [PyMOL] representing missing residues in pymol

Thank you Thomas. Best Regards Priyan On Thu, Sep 25, 2014 at 5:23 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Priyan, > > unfortunately PyMOL doesn't have such functionality to include missing > atoms in the sequence viewer, neither does it read SEQRES records. > > Cheers, >

[PyMOL] 1.7.2.2 bugfix release

Dear all, We released Incentive PyMOL 1.7.2.2 which fixes the mouse wheel issue on Windows and broken putty cartoon representation. Installers can be downloaded from http://pymol.org/download as usual. Open-Source PyMOL was not affected by those issues. Cheers, The PyMOL Team at Schrödinger

Re: [PyMOL] Molecular Visualisation in PyMol

Hi Gian, thank you very much! The idea to associate side chain dynamics with the its B-factor is very attractive for me! However I'm not sure how to make ensemble-like view of the side chains in accordance to its B-factors - in fact as the end of the day (night?!) I'd like to obtain representatio

Re: [PyMOL] representing missing residues in pymol

Hi Priyan, unfortunately PyMOL doesn't have such functionality to include missing atoms in the sequence viewer, neither does it read SEQRES records. Cheers, Thomas On 21 Sep 2014, at 23:28, Priyadarshan wrote: > Hello everyone > > Many a times we have structures solved with residues missin

Re: [PyMOL] measure angles in programming

Hi Lei, those tunnel atoms all have the same name, thus the selection is not unique (not a *single* atom but multiple). For a script like that, it's best to select by atom index. cmd.iterate("tunnel", 'stored.centers.append("(%s`%d)" % (model, index))') Cheers, Thomas On 24 Sep 2014, at 23:

Re: [PyMOL] Shell utilities for structural bioinformatics

>From the previous task it's OK now small question about pymol :) how to prevent removing TER record after editing of the structure using pymol e.g I used the following command to load protein-ligand complex (where there is TER between protein and ligand) and remove hydrogens and than save back

Re: [PyMOL] measure angles in programming

It seems due to the fact that youre selection s is not a valid selection. Try to simplify it by simply giving (model, chain, resi, name) It should be enough to define a single atom, as required by get_angle On 9/25/14 5:27 AM, Lei Chen wrote: > Hi, > I still have trouble. I am not sure if it is