Dear Thomas, thank you for these short and perfect answers.
1. All fine now. 2. Updated the plugin and the GUI bug is gone. One more thing though. Whenever I click the button to either set temporary file locations or to set program locations in APBS GUI window I immediately get a Segmentation fault error (/usr/local/bin/pymol: line 3: 9250 Segmentation fault (core dumped)). 3. Also works great. Thank you again for your quick reply! Your help is invaluable to me (and probably to many other users of Pymol). Keep up the good work! Kind regards, Matic On 13. 01. 2016 20:01, Thomas Holder wrote: Hi Matic, 1. If you have conflicting (non-unique) file names, you have two options: a) Specify an object name with the "load" command (load foo_1.dx, foo_1_map) b) Set the "auto_rename_duplicate_objects" setting 2. The APBS GUI update bug has been fixed in the PyMOL SVN repository two days ago. If you don't want to recompile, you can also install the updated plugin manually from here: http://pymolwiki.org/index.php/Apbsplugin 3. Use the "matrix_copy" command to transfer the transformation matrix from the molecular object to the map object after alignment (matrix_copy foo_1, foo_1_map) Hope that helps. Cheers, Thomas On 13 Jan 2016, at 13:19, Matic Kisovec <matic.kiso...@ki.si><mailto:matic.kiso...@ki.si> wrote: Dear all, I wish to report two issues (numbered 1. and 2.) with APBS plugin in Pymol. I use Xubuntu 14.04 (Xubuntu is a flavour of Ubuntu) and opensource Pymol 1.8.0.0. • First I tried to perform a couple of APBS calculations through the APBS plugin window and all went great. Then I did a batch pdb2pqr transformation on my local machine and then a batch apbs calculation also on my local machine. Both directly in terminal (no connection with Pymol). I more or less followed these instructions: http://jamiebaxter.com/blog/?p=890 . After the calculations I ended up with all the standard files (.in, .pqr and .dx). The issue was that I was not able to load them in Pymol. After loading .pqr and .dx the tab 'Visualization' in APBS plugin windows kept saying to load a molecule and a map. And after clicking the button 'Update' nothing happened. There was no error reported. First I thought there has to be something wrong with the manual procedure of generating .pqr and .dx files. More or less by accident I figured out the problem is in the names of files. I generated them to be iden tical and the only difference was the extension (for example foo_1.pqr and foo_1.dx). If I changed one of the names (I just tried .dx for now) and added or deleted a single character everything went smoothly once loaded in Pymol. Is this a problem/bug only in my case since the APBS plugin also creates temporary files with identical names? • Another possible bug is present in the 'Visualization' tab of APBS plugin. If one uses the button 'Update' in the 'Maps and Molecules' field (the one marked in orange in this image: https://app.box.com/s/wztcwondd0fiqqczdyekhnd3ltfo0nxa) then one slowly loses the option to use the fields 'Positive Isosurface', 'Neg. Isosurface' and 'Molecular Surface'. They keep on moving downwards until you loose the from the screen (see the image in the previous link to see this). 'Field lines' fields keep appearing after each click on the 'Update' button. Of course one can restrain from using the mentioned 'Update' button since it seems to me that it is not really necessary at all. But still it is a strange behaviour. • This is just a question not an issue really. Is there an easy way to visualise multiple aligned proteins with their electrostatic surfaces simultaneously? I tried 'set grid_mode' and it works but not if I do an alignment after loading the pqr structure and the APBS map. I suppose I could/should align them before doing the calculations but since I didn't it would be great if it is possible to do this during visualization. Hopefully somebody can look into this or at least find this through googling and in this way save a couple of minutes or hours. All the best, Matic Kisovec
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