[PyMOL] representing ferrocene in pymol
Dear all, How can I accurately represent ferrocene in pymol, without using CONECT lines in the pdb file ? By accurately I mean at least including the C-C bonds; I'd rather not have any Fe-C bonds, but if they are present I can live. I've been trying to figure out how to do this using atom selections, or trying to get gonds between the nonbonded... Any hints are welcome, all the best Ed. -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb___ 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] representing ferrocene in pymol
How about. import select_sites sites 1a3l set_bond stick_radius, 0.1, resi 213 extract Fe_atom, resi 213 and name Fe Wiki http://www.pymolwiki.org/index.php/Select_sites http://www.pymolwiki.org/index.php/Set_bond Best Troels Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 2013/2/11 Edward Deira edward.de...@gmail.com Dear all, How can I accurately represent ferrocene in pymol, without using CONECT lines in the pdb file ? By accurately I mean at least including the C-C bonds; I'd rather not have any Fe-C bonds, but if they are present I can live. I've been trying to figure out how to do this using atom selections, or trying to get gonds between the nonbonded... Any hints are welcome, all the best Ed. -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ 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 -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb___ 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] freeglut error
Hi. Well, I don't know really what you wan't, but I remember pain with graphics and computers. :-) I see the same error (X Error of failed request) when I get a kernel update to my CentOS comp. That screws up my NVIDIA driver installation, pymol fails, and I have to reinstall the driver package. The term LIBGL_ALWAYS_INDIRECT=1, is controlling something with which method draws the window. By OpenGL or by the mesa driver. (Something like that). The OpenGL is super fast, and mesa driver is slow. Our shared installation of pymol, means that computers with the NVIDIA driver works super fast, while the computers which havent an updated NVIDIA driver is just running slow. (Pain slow). If this can help, our execution script for pymol is: -- [tlinnet@tomat pymolsvn]$ cat pymolMPEG.sh #!/bin/bash if [ ! -f $HOME/.local/share/applications/pymolsvn.desktop ]; then ln -s /ourlab/software/pymolsvn/pymolsvn.desktop $HOME/.local/share/applications/pymolsvn.desktop fi export FREEMOL=/ourlab/software/pymolsvn/svnfreemol/freemol export PYMOL_GIT_MOD=/ourlab/software/pymolsvn/Pymol-script-repo/modules export PYTHONPATH=$PYTHONPATH:/ourlab/software/x64/lib64/python2.6/site-packages/PIL export PYTHONPATH=$PYTHONPATH:/ourlab/software/x64/lib64/python2.6/site-packages/lib-tk export PYTHONPATH=$PYTHONPATH:/ourlab/software/x64/lib64/python2.6/site-packages/lib-dynload export PYTHONPATH=/ourlab/software/pymolsvn/Pymol-script-repo/modules:$PYTHONPATH export PYTHONPATH=/ourlab/software/pymolsvn/Pymol-script-repo:$PYTHONPATH export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/ourlab/software/x64/lib/pymollib *export LIBGL_ALWAYS_INDIRECT=no* /usr/bin/python /ourlab/software/pymolsvn/modules/pymol/__init__.py $@ Best Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 2013/2/7 m.r...@5-cent.us Hi, folks, If there's a howto or FAQ on this, please give me a pointer. We've recently install pymol on several systems. We're running CentOS 6.3, and the yum installed pymos is 1.3.3.20100705svn3911 ssh -Y into other workstations lets me run it with no problem. However, if I do the same to a headless server, on which X is *not* running (if that makes any difference - it is installed), results in freeglut (pymol): ERROR: Internal error FBConfig with necessary capabilities not found in function fgOpenWindow X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 4 (X_DestroyWindow) Resource id in failed request: 0x0 Serial number of failed request: 33 Current serial number in output stream: 36 PyMOL: abrupt program termination. When I first log in, glxgears also doesn't run. Having done a lot of googling, once I execute export LIBGL_ALWAYS_INDIRECT=1 glxgears runs, albeit slowly and irregularly (faster, slower, etc). However, pymol still gives me the same errors (and I have read that there are two of them, the freeglut and the X error. Any solutions? workarounds? Thanks in advance. mark, sysadmin, not researcher -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ 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 -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb___ 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] Zoom + Fading simultaneously in movie
Hi João, You'll need to use the mdo command to fade while zooming. The easiest way is to use the movie_fades script ( http://www.pymolwiki.org/index.php/Movie_fade) from the PyMOLWiki. Cheers, -- Jason On Sat, Feb 9, 2013 at 4:48 AM, João Rodrigues anar...@gmail.com wrote: Hi all, I'm trying to make a short movie here and I came across something I can't find on the internet how to do it.. I want to zoom in a region of the protein (done easily) and at the same time fade its surface (also easily done on its own, thanks Tsjerk). Is this possible or we cannot have two actions in the same frame? Sorry for the limited jargon for movie making! Best, João -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ 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 -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb___ 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] fetch biounits or NMR model
Hi Michael. Something similar has been made to show the SITES labels of a pdb file, for quick referencing of a crystal structure. http://pymolwiki.org/index.php/Select_sites You could look into how that is written, and provide something similar for an NMR structure? Best Troels Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 2013/2/8 Zimmermann, Michael T., Ph.D. zimmermann.mich...@mayo.edu Dear PyMOL Users, ** ** I’ve been using fetch and fetchlocal (from the wiki) for working with multiple datasets of structures, but have a nagging issue that I have not found an efficient way to solve. I typically download the first biological unit, which works for X-ray structures. The trouble is (for good reason), NMR structures don’t have a .pdb1 file. Does anyone have a script to do, or have a good idea about how to implement, the following? (It’s really my lack of familiarity with catching the value from functions like cmd.get_names (rather than it just being printed) in python that’s my barrier…) ** ** Attempt to fetch 2yrq.pdb1 If fetch fails, try fetching 2yrq.pdb If successful and we have 1 state, save the first state ** ** Thanks! ** ** *Michael T. Zimmermann* Ph. D. in Bioinformatics | Health Sciences Research | Division of Biomedical Statistics and Informatics *Mayo Clinic* | 200 First Street SW | Rochester, MN 55905 | mayoclinic.orghttp://www.mayoclinic.org ** ** -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ 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 -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb___ 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] representing ferrocene in pymol
That's pretty slick. Alternatively you can delete the drawn bonds using the builder module. Then show nb_sphere for the Fe atom. If you have access to the CSD I would grab one from there Hope this helps From: Troels Emtekær Linnet [mailto:tlin...@gmail.com] Sent: Tuesday, 12 February 2013 3:17 a.m. To: Edward Deira Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] representing ferrocene in pymol How about. import select_sites sites 1a3l set_bond stick_radius, 0.1, resi 213 extract Fe_atom, resi 213 and name Fe Wiki http://www.pymolwiki.org/index.php/Select_sites http://www.pymolwiki.org/index.php/Set_bond Best Troels Troels Emtekær Linnet Ved kløvermarken 9, 1.thhttp://1.th/ 2300 København S Mobil: +45 60210234tel:%2B45%2060210234 2013/2/11 Edward Deira edward.de...@gmail.commailto:edward.de...@gmail.com Dear all, How can I accurately represent ferrocene in pymol, without using CONECT lines in the pdb file ? By accurately I mean at least including the C-C bonds; I'd rather not have any Fe-C bonds, but if they are present I can live. I've been trying to figure out how to do this using atom selections, or trying to get gonds between the nonbonded... Any hints are welcome, all the best Ed. -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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 -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb___ 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] freeglut error
On 02/11/13 09:30, Troels Emtekær Linnet wrote: Hi. Well, I don't know really what you wan't, but I remember pain with graphics and computers. :-) I see the same error (X Error of failed request) when I get a kernel update to my CentOS comp. That screws up my NVIDIA driver installation, pymol fails, and I have to reinstall the driver package. Nope, not needed. I had not updated the system before the pymol package was installed - it did come as a package from a standard repository. The term LIBGL_ALWAYS_INDIRECT=1, is controlling something with which method draws the window. By OpenGL or by the mesa driver. (Something like that). The OpenGL is super fast, and mesa driver is slow. Yeah, it appears to definitely be freeglut. In googling, I found several references to a variable or function name change. snip If this can help, our execution script for pymol is: -- [tlinnet@tomat pymolsvn]$ cat pymolMPEG.sh #!/bin/bash if [ ! -f $HOME/.local/share/applications/pymolsvn.desktop ]; then ln -s /ourlab/software/pymolsvn/pymolsvn.desktop $HOME/.local/share/applications/pymolsvn.desktop fi export FREEMOL=/ourlab/software/pymolsvn/svnfreemol/freemol export PYMOL_GIT_MOD=/ourlab/software/pymolsvn/Pymol-script-repo/modules export PYTHONPATH=$PYTHONPATH:/ourlab/software/x64/lib64/python2.6/site-packages/PIL export PYTHONPATH=$PYTHONPATH:/ourlab/software/x64/lib64/python2.6/site-packages/lib-tk export PYTHONPATH=$PYTHONPATH:/ourlab/software/x64/lib64/python2.6/site-packages/lib-dynload export PYTHONPATH=/ourlab/software/pymolsvn/Pymol-script-repo/modules:$PYTHONPATH export PYTHONPATH=/ourlab/software/pymolsvn/Pymol-script-repo:$PYTHONPATH export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/ourlab/software/x64/lib/pymollib *export LIBGL_ALWAYS_INDIRECT=no* /usr/bin/python /ourlab/software/pymolsvn/modules/pymol/__init__.py $@ snip I'll look at that tomorrow. One thing I question: why are there asterisks around the export LIBGL_ALWAYS_INDIRECT? mark -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ 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
