[PyMOL] Extra electron denity map is not visible in pymol
Hello everybody I have two different isoforms of a crystals of different of 3.0A (SAD Dataset) and 2.5A resolution. In one crystal form a dimer is present is ASU, where as in another crystal form it is present as a tetramer. I want to make a image which should show the extra elctron density which is present in tetrameric form. This extra density which is visible in coot as well as in O but not in pymol with the same map file. Although i tried unset the normalisation of the ccp4 map, thge map remain as such without extra density of the another molecule. I would appreciate the suggestions. Thanks in advance peter -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] draw the axes
Hello all I am working on a proetin having different domains. I would like to make movie and draw some axis on my structure which represent the axis of libration and translation. Movie would present the domain conformation changes and its relevence with biology. I checked on the pymol wiki but i find hard to make picture like this through pymol. I am novice in scripting. I have enclosed a example image in the attachment.If anybody helps me, i wiould be thankfull. Hello all Thanks in advance peter -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com___ 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] stereo image for publication
Hello all I am making stereo image for the publication purpose. I am going through this procedure. I save both left and right stereo images from the pymol.i use microsift power point bring them ~63mm closer irrespective of their size and save them as a image file.Then i use photoshop to label them and save them as per the journal requirment DPI. problem comes in the photoshop. i cannot maintain the size, DPI as well as stereo image distance simulatneously. Since, 63mm distance should be maintaned for the stereoimage then i have to compromise with DPI or the image size. If i amintain the stereo distance and DPI then i have to compromise with the size. or If i maintain the size and stereo distance then i have to compromise DPI. can anyone help me? How to maintain all stereoimage distance as well as DPI and image size as the journal requires. I would greatly appreciate the help. Thanks in advance Peter -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ 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] label a stereo .png image in pymol
Hello all I have made a stereo image in pymol and photoadobeshop. But, i would like to label the image file which should like a stereo image label. how that can be done in the pymol. I can do it in photoadobeshop .problem lies her that i am not sure is the labels are really stereo or not? can anyone suggest solutions. I would appreciate that. Thanks in advance peter -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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 zoom during movie
HEllo all I am trying to make a movie , in which i would like to rotate the struture at X-axis, rather than Y-axis and followed by zoom out of the particular state of the frame to make more realistic and expalnatory. I looked into pymol wiki as well as tutorial of the pymol. I could make the rotation ofthe structure at Y-axis but not at X-axis and simultaneously i am not able to zoom out the particular state. I am using the educational version of the pymol1.1. I also tried eMovie. can any one suggest some ideas. I would be thankfull. Thanks in advance regards peter -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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] rotation axis representation with arrows and shaft
Hi all I am working with a multidomain protein. which is present in closed and open conforamtion because of the motion in the domains of the protein. I would like to describe the roation angle of the different domains of the protein and the direction of the domain motion of my structure as a pictorial representation. I know the rotation angles and the direction of motion. My major problem is the represtion in picture with arrows and shaft with the cartoon diagram. I donot know which program can do this. Is it this can be done with pymol? I know that Dyndom can do everything, but here again i am not aware with the represetion of the domain motion with arrows and shaft. i would appreciate the suggestions. Thanks in advance Peter
[PyMOL] selection partcular part of the model
Hello I would like know, how can i show the electron density map of the only selcted part along with my ligand in pymol. I donot like to show the extra density. I guess isomesh map, selction site may help, but i would be interested in detail of it. I would appreciate the suggestions. Thanks in advance peter
[PyMOL] problem in showing the electron density map
Hello all I am trying to upload the ED map on pymol. but, it is not visible on the screen. Although i checked at pymol wiki and i did as it is given on the wiki. For example. I took ccp4 format map and coverted it into xplor format with mapman.(beacuse i tried with ccp4 format map with test_file.map as well as test_file.ccp4 maps, but pymol showed this kind of error. I begin like this- load test_file.xplor, test_file isomesh map, test_file, 2.0, site, carve=1.6 But, it doesnot show up on the screen. I am writing the pymol taskbar reponse. 1) loading of the map file It has been loaded sucessfully, and shows this kind of information on task bar. - mdException Exception in Tk callback Function: > (type: ) Args: () Traceback (innermost last): File "/home/soft/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/home/soft/pymol/modules/pmg_tk/skins/normal/__init__.py", line 438, in file_open self.cmd.load(ofile,quiet=0) File "/home/soft/pymol/modules/pymol/importing.py", line 496, in load raise pymol.CmdException CmdException: Crystal: Unit Cell 54.064 84.618 101.215 Crystal: Alpha Beta Gamma90.000 90.000 90.000 Crystal: RealToFrac Matrix Crystal:0.0185 -0. -0. Crystal:0.0.0118 -0. Crystal:0.0.0.0099 Crystal: FracToReal Matrix Crystal: 54.06400.0. Crystal:0. 84.61800. Crystal:0.0. 101.2150 Crystal: Unit Cell Volume 463037. ExecutiveLoad: "/home/peter/test_file.xplor" loaded as "test_file", through state 0. 2. generation of map-- isomesh map, test_file, 2.0, site, carve=1.6 -- PyMOL>load test_file.xplor, test_file Crystal: Unit Cell 54.064 84.618 101.215 Crystal: Alpha Beta Gamma90.000 90.000 90.000 Crystal: RealToFrac Matrix Crystal:0.0185 -0. -0. Crystal:0.0.0118 -0. Crystal:0.0.0.0099 Crystal: FracToReal Matrix Crystal: 54.06400.0. Crystal:0. 84.61800. Crystal:0.0. 101.2150 Crystal: Unit Cell Volume 463037. ExecutiveLoad: "test_file.xplor" loaded as "test_file", through state 0. PyMOL>isomesh map, test_file, 2.0, site, carve=1.6 Selector-Error: Invalid Selection Name. ( site )<-- Executive: object "map" created. Isomesh: created "map", setting level to 2.000 ObjectMesh: updating "map". --- But, finally map doesnot show up. What could be the problem. Suggestions would be appereciated. Thanks in advance Peter
