[PyMOL] assigning properites
Hello, I was wondering if anyone out there has connived a way to assign different properties to different objects (properties that are normally universal)? For example, setting cartoon_trace to different values so one could draw cartoons for CA-only and full atomic models in the same session. Thanks in advance, Frank Long time listener, 1st time poster -- Frank Murphy MRC LMB Structural Studies Division Hills Road Cambridge CB2 2QH LAB +44 1223 402295 MOB +44 7779 224206 FAX +44 1223 213556 SKYPE frankvmurphy
Re: [PyMOL] assigning properites
Hi Frank, These settings apply to objects, if specified. set cartoon_trace,1,object1 will make it apply only to object1 Cheers, Tsjerk On 5/23/06, Frank Murphy f...@mrc-lmb.cam.ac.uk wrote: Hello, I was wondering if anyone out there has connived a way to assign different properties to different objects (properties that are normally universal)? For example, setting cartoon_trace to different values so one could draw cartoons for CA-only and full atomic models in the same session. Thanks in advance, Frank Long time listener, 1st time poster -- Frank Murphy MRC LMB Structural Studies Division Hills Road Cambridge CB2 2QH LAB +44 1223 402295 MOB +44 7779 224206 FAX +44 1223 213556 SKYPE frankvmurphy --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336
[PyMOL] Is there any way to show the coordinates?
Hello All, Is there any way to show the coordinates for the orientation that a protein is in? Lets say you tweak (rotate and turn) a protein in to a particular orientation, is there any way to tell pymol to display the coorindates for that orientation. So that you could just manually input those coordinates and have pymol automatically orient the protein to return to that orientation. Thanks for your help. Ron
Re: [PyMOL] Is there any way to show the coordinates?
Hi Ron, Check the commands get_view set_view Cheers, Tsjerk On 5/23/06, Ronald Chiu rccom...@gmail.com wrote: Hello All, Is there any way to show the coordinates for the orientation that a protein is in? Lets say you tweak (rotate and turn) a protein in to a particular orientation, is there any way to tell pymol to display the coorindates for that orientation. So that you could just manually input those coordinates and have pymol automatically orient the protein to return to that orientation. Thanks for your help. Ron -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336
[PyMOL] alternate conformations
Hi, I would like to represent my alternate conformations by showing one residue in dashed sticks and the other in solid sticks. Can anyone help me with that? Tina Nguyen Graduate Student University of Massachusetts Medical School
RE: [PyMOL] biological unit
Hi Jacob, Thank you so much for your reply! Actually, I want to show how the virus HK97 evolve from Prohead (PDB ID: 1if0) to Head (PDB ID: 1ohg) state. There are some intermediate states from our calculation. All the PDB files are Biological Unit files. However, if you load a biological unit file to PyMOL, it will be put into separated states/frames. By applying the command, 'split_states', to the first PDB file, [1if0.pdb1], you will get a series of objects, e.g.: 1if0_0001 1if0_0002 1if0_0003 .. 1if0_0060 After that if you now load the second PDB file, [1ohg.pdb1], and split it, you will get more objects: 1ohg_0001 1ohg_0002 .. 1ohg_0060 All the above objects appear in the same state/frame. But we want to put the N'th file to the N'th frame. Is there an easy way to put the second Biological Unit PDB file to next states/frame? Thank you all! Best, Zheng -Original Message- From: Jacob Corn [mailto:jc...@berkeley.edu] Sent: Tuesday, May 23, 2006 11:12 AM To: proteiny...@gmail.com Subject: Re: [PyMOL] biological unit Hi Zheng, Sorry it's taken me a while to get back to you. I'm not entirely clear on your question. Precisely what is it that you're trying to do with the movie? I don't think split_states has an option to keep some of the states as separate states while splitting others, if that's what you're asking. You could split everything and then write a script to use only certain of those resulting models in the movie. Zheng Yang wrote: Dear all, I want to create a movie of a virus capsid from N biological unit pdb files (N frames). After loading and splitting the first pdb file, how to load the remaining pdb files and put them in different states/frames? Is there any optional control on the command, 'split_states', e.g. splitting to a certain state? Thanks a lot! Zheng -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Jacob Corn Sent: Sunday, May 21, 2006 1:58 AM To: surendra negi Cc: PyMOL-users@lists.sourceforge.net Subject: Re: [PyMOL] biological unit Hi Surendra, Just to make sure, are you downloading the biological unit PDB from RCSB? That should be a 5MB gzipped file. The normal PDB for 1c8e does not contain coordinates for the biological unit (which you need to use split_states); only a monomer and then info on crystal symmetry. If you go to a PDB entry at the RCSB and open up the Download Files menu, choose the last option in the list, Biological Unit Coordinates. Here is a direct link to the biological unit for 1c8e http://www.rcsb.org/pdb/files/1c8e.pdb1.gz The normal PDB is http://www.rcsb.org/pdb/files/1c8e.pdb.gz Jacob surendra negi wrote: Ji Jacob, I am trying to produce the results shown in http://delsci.com/img/1c8e.jpg http://delsci.com/img/1c8e-screen.jpg using split_states 1c8e delete 1c8e zoom spectrum b hide lines set cartoon_sampling,3 show cartoon bg_color grey70 set hash_max, 150 ray orient zoom complete=1 ray script in my linux machine but is is not working and also giving no error message. It is just showing me single molecule. Do you have any suggestions. thanks surendra __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] alternate conformations
Tina, A work-around that does something like what you are looking for is: load protein_with_alts.pdb, A load protein_with_alts.pdb, B hide everything, show sticks, A and alt A show sticks, B and alt B set stick_ball, 1, B set stick_overlap, -1.8, B Cheers, -bob On 5/23/06, Nguyen, Tina (GSBS) tina.ngu...@umassmed.edu wrote: Hi, I would like to represent my alternate conformations by showing one residue in dashed sticks and the other in solid sticks. Can anyone help me with that? Tina Nguyen Graduate Student University of Massachusetts Medical School
[PyMOL] AMD64 X2+Quadro FX1300+Fedora5
Dear all, I thought to be worth posting this message for those who experience problems with dual core+quadro FX. It seems that only recently kernel and compatible driver became available. We succeeded installing PyMOL in a AMD64 X2+Quadro FX1300+Fedora5. After installing Fedora 5 (which seems to recognize FX1300 automatically but without working properly), we followed a recipe (2-May-2006) from http://www.fedorafaq.org/ (Problems and Their Solutions, Q3) We used yum install kmod-nvidia (yum install kmod-nvidia-smp did not work) Kernel 2.6.16-1.2122_FC5 was installed by this last command line. (21-May-2006 - http://download.fedora.redhat.com/pub/fedora/linux/core/updates/5/i386/) After that, we have followed the rest of the recipe and changed /etc/X11/xorg.conf (Driver nvidia) PyMOL 0.99 runs beautifully although stereo mode was not tested yet. Kind regards, Ricardo Aparicio http://www.iqm.unicamp.br/profs/aparicio.html
[PyMOL] label in Greek letters
Hi All users, I am a PyMOL ver.0.99rc6 (Win and Linux) user. Now I want to label with chain ID ( A, B, G,... for alpha, beta, gamma,...) in Greek letters. I have tried it following http://www.pymolwiki.org/index.php/Label#UTF8_Fonts , but the output corresponds to \316\261 has not been printed. Please give me some advice about this and tell me any other ways to do. Thank you, Arakawa
[PyMOL] Runtime Error
Dear All, Does anyone have the same runtime error, by applying the command, [ray] or [show surface], on big size protein, e.g. 1AON, etc? PyMOL Version: 0.99 System: Dell 9100 OS: Windows XP + SP2 CPU: Intel P4 3.0G RAM: 1.5G Video Card: nVidia GeForce 6800, 256M Thanks, Zheng attachment: Runtime Error.jpg
