Re: [PyMOL] Finding distances along molecular tunnels
Hi Sajeewa, [...] If I follow wizard -- measurements -- distance it asks for atoms to click on, but as the tunnels are empty space when I click on the starting points of the tunnels nothing is recognized. What would be the most accurate way of measuring the above two distances? The tunnel is not really empty space, it's actually composed of pseudo-atoms and it's just a matter of visual representation. Hiding the surface and showing lines should be sufficient. hide surface show lines Now try to use the measurement wizard. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ 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] hide tube / show only filled nucleic acid rings
Have you tried this: http://www.pymolwiki.org/index.php/Examples_of_nucleic_acid_cartoons Best Troels Emtekær Linnet 2012/4/2 Francis E Reyes francis.re...@colorado.edu Tricky one I tried hide cartoon, name P but no go.. instead cartoon skip will do it. On Apr 2, 2012, at 2:50 PM, Eike Schulz wrote: Hello everybody, I am looking for a way to display nucleic acids in cartoon mode but without showing the backbone trace. Unfortunately set cartoon_tube_radius=0 leaves a thin line behind. Thanks a lot in advance Best Eike -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ 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 -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ 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 -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ 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] problem installing pymol plugin
Hi Vaibhav, First: I assume you did NOT copy the PocketPickerScript to C:\Program Files\DeLano Scientific\PyMOL\modules\pmg_tk\startup, otherwise there would not be a No such file error. Second: The plugin does not use the best coding style, it has hard coded file paths. So I would not be surprised if you will encounter more errors when using it. However, the plugin works for me on my Linux box after some modifications. Also, there is no version command in PyMOL, but a get_version command. Hope that helps. Cheers, Thomas On 04/03/2012 05:50 AM, vaibhav dixit wrote: Dear Pymol users, I am using pymol for modeling purposes. I wanted to display active site shape in my report. So I cam across your programm pocketpicker. I followed the procedure given on page http://gecco.org.chemie.uni-frankfurt.de/pocketpicker/PocketPicker_Readme.pdf But unfortunately the plugin is not getting installed. I am using windows vista OS. Please suggest on how to install it correctly? Thank you. Following is the message displayed. PyMOLversion Traceback (most recent call last): File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py, line 455, in parse exec(layer.com2+\n,self.pymol_names,self.pymol_names) File string, line 1, in ? NameError: name 'version' is not defined PyMOLrun C:\Program Files\DeLano Scientific\Pymol\modules\pmg_tk\startup\PocketPickerScript\LigandKicker_1.0.py http://ligandkicker_1.0.py/ Traceback (most recent call last): File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py, line 332, in parse parsing.run_file(exp_path(layer.args[0]),self.pymol_names,self.pymol_names) File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py, line 455, in run_file execfile(file,global_ns,local_ns) IOError: [Errno 2] No such file or directory: 'C:\\Program Files\\DeLano Scientific\\Pymol\\modules\\pmg_tk\\startup\\PocketPickerScript\\LigandKicker_1.0.py http://ligandkicker_1.0.py/' -- With regards Vaibhav A. Dixit Ph.D. Scholar Department of Medicinal Chemistry Natl. Inst. Pharm. Edu. Res. (NIPER) Sector 67, Phase X, S.A.S. Nagar (Mohali) Punjab -160 062 INDIA Phone (Mobile): +919915214408 E-mail: vaibhavadi...@gmail.com mailto:vaibhavadi...@gmail.com www.niper.nic.in http://www.niper.nic.in -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ 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] Protein Parameters?
Hi, This is unrelated to PyMol, but I just wanted to spam the community to see what they think about different protein parameters. Let me know if this sort of question is inappropriate for the forum. I have thousands of randomly generated 7 amino acid peptide sequences that are within a virus. As we subject this virus to reproduction selective pressure in cell lines, we get back functional viruses with certain 7 amino acid sequences, while most random sequences are null mutations. So I am now testing the the positive sequences to see what they have in common, or what is most important. I am doing this with a likely structural sequence and a likely surface sequence. So far I have these params from http://web.expasy.org/protparam/ and ConSurf 1) Isoelectric Point 2) Molecular Weight (may mean bulkiness) 3) GRAVY: grand average of hydropathicity 4) Conservation of AAs at given locations Do any of you protein experts know of other parameters that I could be testing? Maybe something like Phi-value analysis? -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ 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] Protein Parameters?
Hi Shane, Whilst I am no expert, I would think possible a sequence motif (based on amino acid composition) may help. It may show up certain amino acids at specific points. Given the short length of the peptides, the question is what are they used for? Hope this helps _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 From: Shane Neeley [mailto:shane.nee...@gmail.com] Sent: Wednesday, 4 April 2012 3:58 a.m. To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Protein Parameters? Hi, This is unrelated to PyMol, but I just wanted to spam the community to see what they think about different protein parameters. Let me know if this sort of question is inappropriate for the forum. I have thousands of randomly generated 7 amino acid peptide sequences that are within a virus. As we subject this virus to reproduction selective pressure in cell lines, we get back functional viruses with certain 7 amino acid sequences, while most random sequences are null mutations. So I am now testing the the positive sequences to see what they have in common, or what is most important. I am doing this with a likely structural sequence and a likely surface sequence. So far I have these params from http://web.expasy.org/protparam/ and ConSurf 1) Isoelectric Point 2) Molecular Weight (may mean bulkiness) 3) GRAVY: grand average of hydropathicity 4) Conservation of AAs at given locations Do any of you protein experts know of other parameters that I could be testing? Maybe something like Phi-value analysis? -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ 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] Application deadline approaching: CCP4 summer school at APS, in USA
Dear Colleagues, We would like to point out that the application deadline for the 5th annual CCP4 Summer School From data collection to structure refinement and beyond is April 17, 2012. The school will take place from June 19 through June 26, 2012 at the Advanced Photon Source (APS) near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (The program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2012/index.php The school will cover all aspects of macromolecular structure determination and validation. Some of the world's leading experts will be providing instruction and hand-on help. We are looking forward to another productive school this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ 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] Protein Parameters?
Hi Shane, I think I meant weblogo which shows frequency of amino acids e.g. http://weblogo.berkeley.edu/ Sorry for the confusion J _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 From: Shane Neeley [mailto:shane.nee...@gmail.com] Sent: Wednesday, 4 April 2012 10:18 a.m. To: Joel Tyndall Subject: Re: [PyMOL] Protein Parameters? Hi Thanks for the tip Joel. I checked a few of the sequences for protein motifs but because they are so sort and because there really is no known function, i think it is unlikely to have any hits. On Tue, Apr 3, 2012 at 2:58 PM, Joel Tyndall joel.tynd...@otago.ac.nzmailto:joel.tynd...@otago.ac.nz wrote: Hi Shane, Whilst I am no expert, I would think possible a sequence motif (based on amino acid composition) may help. It may show up certain amino acids at specific points. Given the short length of the peptides, the question is what are they used for? Hope this helps _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293tel:%2B64%203%204797293 Fax / Waeawhakaahua +64 3 4797034tel:%2B64%203%204797034 From: Shane Neeley [mailto:shane.nee...@gmail.commailto:shane.nee...@gmail.com] Sent: Wednesday, 4 April 2012 3:58 a.m. To: pymol-users@lists.sourceforge.netmailto:pymol-users@lists.sourceforge.net Subject: [PyMOL] Protein Parameters? Hi, This is unrelated to PyMol, but I just wanted to spam the community to see what they think about different protein parameters. Let me know if this sort of question is inappropriate for the forum. I have thousands of randomly generated 7 amino acid peptide sequences that are within a virus. As we subject this virus to reproduction selective pressure in cell lines, we get back functional viruses with certain 7 amino acid sequences, while most random sequences are null mutations. So I am now testing the the positive sequences to see what they have in common, or what is most important. I am doing this with a likely structural sequence and a likely surface sequence. So far I have these params from http://web.expasy.org/protparam/ and ConSurf 1) Isoelectric Point 2) Molecular Weight (may mean bulkiness) 3) GRAVY: grand average of hydropathicity 4) Conservation of AAs at given locations Do any of you protein experts know of other parameters that I could be testing? Maybe something like Phi-value analysis? -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ 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
