[PyMOL] spectrum colouring for dashes?
Dear Pymol Users, I'm creating dashes between atoms via the distance command. So far I have always indicated the size of the distance simply by the label that pops up automatically with the distance command. I was wondering however whether it is actually possible to also colour dashes according to their distance size. I'm looking for something similar to the cmd.spectrum command for colouring atoms according to their b-factor or occupancy value. Big thanks for your help in advance. Abdullah ---@ Dr. Abdullah Kahraman PostDoc Aebersold - Malmstroem Group Institute of Molecular Systems Biology ETH Zurich HPT C75 Wolfgang-Pauli-Str. 16 8093 Zurich Switzerland http://www.imsb.ethz.ch/researchgroup/malars/people/abdullah_kahraman abdul...@imsb.biol.ethz.ch work: +41-(0)44-633 39 45 mobile: +41-(0)76-317 0305 -- 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] Secondary structure motifs
Hi James, The 2D representation of secondary structures you show, is not possible with PyMOL. You would need to extract the secondary and code up the solution yourself. I bet there are servers out there that will do this for you, Cheers, -- Jason On Sun, Nov 20, 2011 at 11:20 AM, James Starlight jmsstarli...@gmail.com wrote: Dear PyMol Users! I wounder to know about possible options for working with elements of secondary structure of my pdb. E.g I want to obtain topology representation of my protein like tihs http://strees.protres.ru/Top.%20photos/2.2.gif Is there any plugin for PyMol wich could help me with this ? Could you also show me tutorial where I could found possible examples working with the SS elements? Thanks, 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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] Pymol on Intel HD Graphics 3000
The problem disappears upon upgrading from Opensuse 11.4 (running kernel 2.6) to OpenSuse 12.1 (running kernel 3.1). -- 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] Work with pdb's enssemble
Jason, but as I've understood super did alignment only for two structures, Is there any way to do the same operation for ensemble ? (for CE as I understood this could be done by alignto command but it lack for seq alignment iin this case) James 2011/11/21 Jason Vertrees jason.vertr...@schrodinger.com Hi James, set fetch_host, pdbe Your PyMOL looks to be outdated. This was added to the open-source in v1.3r1, I think. By the way could you also help me with the alignment of my structure ( I've posted this question today at this topic). I think that I should use the combination of the structure alignment ( like CEalign) with the common seq. alignment but I dont know exactly how :( You should use the 'cealign' or 'super' commands to do this. Cealign uses only structure, whereas 'super' uses both structure and sequence. Please continue to post questions like this to the list for best results: there are some very smart people on our PyMOL list. Cheers, -- Jason James 2011/11/21 Jason Vertrees jason.vertr...@schrodinger.com James, 1) I've already tried to use it but the downloading was to slow. How I can change source for pdb downloading ? E.g set fetch_host didnt worked :( set fetch_host, pdbe should work. Please let me know if it doesn't. 2) How I can specify individual chain for uploading via fetch command? You can't--PyMOL downloads the entire structure. To show just a given chain type something like: fetch 1hpv # c. A means chain A color blue, c. A Use similar selectors, for example # remove all atoms from the structure # except those in chain B remove not chain B Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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] query
here it is: http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts vitali On Mon, Nov 21, 2011 at 8:50 AM, rjayashree13-scie...@yahoo.co.in rjayashree13-scie...@yahoo.co.in wrote: Thank you. It works, but it does not bring out the type of interaction responsible for interface contact-hydrogen bonding or electrostatic interaction etc. I am using another tool called PSAP for analyzing inter-molecular interactions (iris.physics.iisc.ernet.in/psap) It gives me the residues involved in hydrogen bonding, now using Pymol I can label these residues, but is there any way to depict these hydrogen bonds also and the distances? Dr. Jayashree Ramana http://www.juit.ac.in/bio/jsr.php -- *From:* Vitali Stanevich stanev...@wisc.edu *To:* rjayashree13-scie...@yahoo.co.in rjayashree13-scie...@yahoo.co.in *Cc:* pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net *Sent:* Sunday, 20 November 2011 1:57 PM *Subject:* Re: [PyMOL] query check this out: http://www.pymolwiki.org/index.php/InterfaceResidues if you want faster and easier, but less reliable (in my opinion) way, you can analyze your .pdb with PISA: http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html vitali On Sun, Nov 20, 2011 at 1:51 AM, rjayashree13-scie...@yahoo.co.in rjayashree13-scie...@yahoo.co.in wrote: I have a PDB file for a dimeric protein. Is it possible to depict the intersubunit contacts for any PDB file? Is Pymol alone sufficient for this purpose or will it only help visualization? Could you also tell me which commands in Pymol can I use for this purpose? I have tried a lot but could not get an answer to this. I will be very thankful for the favour. Dr. Jayashree Ramana http://www.juit.ac.in/bio/jsr.php -- 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
[PyMOL] how to manually dock protein with DNA
Hi all, I want to manually dock a protein with a piece of DNA. I found in a previous post that it could be done by opening two PDB and shift-middle click-and-drag on the molecule to translate and shift-left-click-and-drag to rotate. I opened both PDBs, and when I pressed shift, and click on the molecule I want to move, and middle click and drag, it didn't translate the molecule, but only draws a box I didn't know what I did wrong. Any idea? Thank you so much! Best, Wei -- 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] how to manually dock protein with DNA
By the way, I am using mac pymol... On Mon, Nov 21, 2011 at 5:07 PM, Wei Shi wei.shi...@gmail.com wrote: Hi all, I want to manually dock a protein with a piece of DNA. I found in a previous post that it could be done by opening two PDB and shift-middle click-and-drag on the molecule to translate and shift-left-click-and-drag to rotate. I opened both PDBs, and when I pressed shift, and click on the molecule I want to move, and middle click and drag, it didn't translate the molecule, but only draws a box I didn't know what I did wrong. Any idea? Thank you so much! Best, Wei -- 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] how to manually dock protein with DNA
Hey Wei, have you set your mouse to Editing mode? Do this first via the application menu Mouse-3 Button Editing and then repeat the steps you described. Cheers, Abdullah On 21 Nov 2011, at 23:07, Wei Shi wrote: Hi all, I want to manually dock a protein with a piece of DNA. I found in a previous post that it could be done by opening two PDB and shift-middle click-and-drag on the molecule to translate and shift-left-click-and-drag to rotate. I opened both PDBs, and when I pressed shift, and click on the molecule I want to move, and middle click and drag, it didn't translate the molecule, but only draws a box I didn't know what I did wrong. Any idea? Thank you so much! Best, Wei -- 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 ---@ Dr. Abdullah Kahraman PostDoc Aebersold - Malmstroem Group Institute of Molecular Systems Biology ETH Zurich HPT C75 Wolfgang-Pauli-Str. 16 8093 Zurich Switzerland http://www.imsb.ethz.ch/researchgroup/malars/people/abdullah_kahraman abdul...@imsb.biol.ethz.ch work: +41-(0)44-633 39 45 mobile: +41-(0)76-317 0305 -- 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] PyMOL 1.5 release
On 15:47 Thu 10 Nov , Jason Vertrees wrote: As has always been the case, some new features added to Incentive PyMOL v1.5.0 will not be immediately added to the open-source project, as Incentive subscribers pay to have priority access to these new features. I always wonder, are there actually people who feel they gain some sort of competitive advantage by having access to PyMOL features first? Doesn't seem to make sense because anyone else can pay for the same level of access. Plus it's mostly a visualization tool, so I'm not sure I understand the rationale. I'd always thought that the payment was intended for people who wanted to support the future of PyMOL as well as get some high-quality documentation and increased personal support. -- Thanks, Donnie Donald S. Berkholz, Ph.D. Research Fellow James R. Thompson lab, Physiology Biomedical Engineering Grazia Isaya lab, Pediatric Adolescent Medicine Mayo Clinic ___ Medical Sciences 2-66 200 First Street SW Rochester, MN 55905 office: 507-538-6924 cell: 612-991-1321 pgpqbXwCHmq7U.pgp Description: PGP signature -- 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
