Re: [PyMOL] H-bonds representation
While the single acceptor H-bond is most common, bifurcated (or three-centred) H-bods are not uncommon in crystal structures, as described starting page 22 of GA Jeffrey's book: http://www.amazon.com/Introduction-Hydrogen-Bonding-Physical-Chemistry/dp/0195095499/ref=sr_1_2?ie=UTF8&qid=1322331503&sr=8-2 James Starlight wrote: > Thomas, thank you for so detailed explanation. > > This way works good but I'd like to ask you about possibe Hbonds in the > protein chain. > > As I remember for protein physics courses the H atom is always donor for only > ONE H-bond ( > and O or N atoms could be akceptors for 1 or 2 Hbonds) > > But In my case there are some cases where H atom ( white ) is donor for the 2 > Hbonds. By > the way I found the same on the picture in WIKI too. > > How it could be explaned ? > > James > > > -- > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > > > > ___ > 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 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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] H-bonds representation
Thomas, thank you for so detailed explanation. This way works good but I'd like to ask you about possibe Hbonds in the protein chain. As I remember for protein physics courses the H atom is always donor for only ONE H-bond ( and O or N atoms could be akceptors for 1 or 2 Hbonds) But In my case there are some cases where H atom ( white ) is donor for the 2 Hbonds. By the way I found the same on the picture in WIKI too. How it could be explaned ? James -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ 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] Editing of the pdb structure
Dear all! :) I need to merge two chains in one pdb ( object) into one united chain. How I could do it? Thanks James 2011/11/18 Joel Tyndall > James, > > ** ** > > Please post this to the bulletin board. You can try to click on the word > (residues usually default) at the bottom right of the viewer. > > ** ** > > Joel > > ** ** > > *From:* James Starlight [mailto:jmsstarli...@gmail.com] > *Sent:* Thursday, 17 November 2011 7:52 a.m. > > *To:* Joel Tyndall > *Subject:* Re: [PyMOL] Editing of the pdb structure > > ** ** > > Another question about working with the structure. > > > I have structure of the fulerene molecule wich consist of 60 carbon atoms > > I switch to the Sequence mode-> Atoms and try to select individual carbon > atoms ( e.g I want to find where this atom situated in my molecule). But > instead of selection of the individual carbons the whole molecule was > selected. How I can work with individual atoms of my structure ? > > James > > 2011/11/15 James Starlight > > Thanks Joel, it's clear now :) > > ** ** > > 2011/11/14 Joel Tyndall > > See attached. > > > > To switch to editing mode click on 3 button viewing or use the menu > > > > Mouse > 3 button editing > > > > > > > > > > > > *From:* James Starlight [mailto:jmsstarli...@gmail.com] > *Sent:* Monday, 14 November 2011 8:44 p.m. > *To:* Joel Tyndall > *Subject:* Re: [PyMOL] Editing of the pdb structure > > > > Dear all, thank you for the advises :) > > Thomas, > > when I've tried to add ACE cap to the N-tem of the first residue of my > peptide I've obtain > > Error: unable to load fragment ''. > > So how I should define dirr from wich those caps groups will be loaded? > > > Joel, > > I could not find such buiilder button :o > > when I've tried to select individual atoms from my FOR residue ( from > sequence panell), the overal residue with all atoms was selected instead :o > > James > > 2011/11/11 Joel Tyndall > > Hi James, > > > > If I am correct in reading what you want you wish to change the FOR group > to an ACE. > > > > I am using a PC version 1.3. Click on the builder button (right hand side > of grey GUI) > > Make sure you are in Mouse mode: 3 button editing. > > > > Click on the carbon of the FOR group and also the oxygen ( a white ball > will appear on each atom) > > Then in the GUI click on the || icon adjacent to “bonds create”. This will > give you the carbonyl. > > Now click on the hydrogen attached to the carbonyl carbon and then click > in the GUI, the carbon atom C. > > This has now created your Acetylated nitrogen. > > > > Then save molecule as: and you can edit the text file to change For to ACE. > > > > > Given this is some sort of dimer, I have just noticed that the second > chain will overlap with the first. > > > > Hope this helps > > > > Joel > > > > *From:* James Starlight [mailto:jmsstarli...@gmail.com] > *Sent:* Friday, 11 November 2011 1:44 a.m. > *To:* pymol-users@lists.sourceforge.net > *Subject:* [PyMOL] Editing of the pdb structure > > > > Dear PyMol Users! > > > > Recently I've opened such topic but I didnt obtain answer on this question > so I try to paraphrase my task. Also I want to specify this topic on > questions lincked with the processing of pdbs. > > 1) I need to remove some elements fron my structure described as the > individual residue and place another element of the same size on the place > of the first element. > > In particular I have two different peptides both of wich have small cap > groups on C and N termi. ( attached) > > I need to remove all caps ( two caps FOR and ETA because there are two > identical chains in that structure) from the 1MAG structure and build > exactly on this place another cap groups wich I'd like to copy from the > second peptide ( KALP). So I'd like to change FOR- > ACE and ETA-> NH2 > twisely for the 1MAG dtructure > > How I can perform such task in PyMol? > > James > > > > ** ** > > ** ** > -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ 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] sterioscopic 3D using ATI HD6800 under linux
Hi All, I would like to have sterioscopic 3D support under linux. I know this can be done with a nvidia Quadro card, as shown on your supported platform page: http://pymol.org/support/platforms I have found that the HD6800 series from AMD has support for sterioscopic 3D and Quad Buffered OpenGL. See the below links for details: http://3dvision-blog.com/ati-has-announced-its-open-stereo-3d-initiative-at-gdc-2010/ http://69.65.116.162/discussions.x/19853 Before I go out and buy a new PC, I would like to know if the HD6800 series can actually create a sterioscopic 3D image under linux. Could anybody tell me if this works? Maybe a bit off-topic on this list, are there any linux games that use sterioscopic 3D? Best regards and thanks in advance, Cedric -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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] H-bonds representation
Hi James, > As I've understood there are no posible ways to represent H-bonds in > proteins in explicit manner. So I'm looking for possible way to do it > via some plugin or another way. PyMOL can find polar contacts and represent them as dashed lines. You don't need any extra plugin. http://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts It's the "distance" command with mode=2 that does the job. http://pymolwiki.org/index.php/Distance There are various dash_* settings that control the appearance of the dashed lines: http://pymolwiki.org/index.php/Dash_Length http://pymolwiki.org/index.php/Dash_color (and many others...) > In particular I need > 1) to visualize H-bonds in some structural motifs like coiled coil wich > are dimers of alpha helices ( so I'd like to see H-bonds beetwen > separate alpha helices ) Try this (lets say helix 1 is resi 1-100 and helix 2 is resi 101-200): # add hydrogens (if not already present) h_add donors # detect polar contacts distance hb_coiled_coil, resi 1-100, resi 101-200, mode=2 > 2) to visualize H-bonds in spicified SS structure ( e.g during formation > of the alpha helices)- so I'd like to see H-bonds beetwen amide and > Carboxy groups in specified amino acid sequence. just like example 1, but with other selections: distance hb_backbone, name O, name N, mode=2 > 3) Finally I'd like to check H-bond in protein-ligand complex ( beetwenn > specified ligand groups as well as some amino acid residues of the > ligand binding pocket) just like before, but with ligand as selection 1 and receptor as selection 2. Hope that helps. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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
