[PyMOL] nice DNA pdb and ring options
I have three questions I'm hoping someone can help with. 1. Does anyone have, or can anyone point me to a program that will generate a nice pdb file that contains 50 or so base pairs of random sequence B form DNA with hydrogen bonds between the bases or no H bonds? I need to be able to scultp the DNA and have one strand react to the pulling of the other strand. I also want to show the union of the AT and GC via H bonds. The H bonds can be regular bonds (and probably will have to be if I'm going to be sculpting). I can make the h bonds and make them real bonds for the sculpting, I'm just wondering of anyone has already done it or has a script around 2. When showing a cartoon of DNA the ribose ring in the backbone is always there no matter which setting you choose. How can I make the phosphates and the ribose rings show as a backbone cartoon tube and keep just the bases as filled sticks with rinngs? 3. Rings on DNA and RNA can be filled, in cartoon mode. But I can't get the rings to fill in on selected amino acids (H, W, Y, F) in a protein of that same file. Is there a fill amino acid ring setting? Thanks in advance for anything you can offer, Adam -- ___ H. Adam Steinberg Artist, Scientist http://adam.steinbergs.us Information Technology and Media Center Department of Biochemistry University of Wisconsin-Madison 433 Babcock Drive Madison, WI 53706 608/265-4982 ___
Re: [PyMOL] nice DNA pdb and ring options
Hello You can look into 3DNA out of Rutgers (http://rutchem.rutgers.edu/~xiangjun/3DNA/). To make the image you describe you will also need to use Raster3D. 3DNA has some basic scripts for this but you will need to write your own to get the image you describe. Andrew On Mon, Feb 23, 2009 at 11:29 AM, H. Adam Steinberg a...@steinbergs.us wrote: I have three questions I'm hoping someone can help with. 1. Does anyone have, or can anyone point me to a program that will generate a nice pdb file that contains 50 or so base pairs of random sequence B form DNA with hydrogen bonds between the bases or no H bonds? I need to be able to scultp the DNA and have one strand react to the pulling of the other strand. I also want to show the union of the AT and GC via H bonds. The H bonds can be regular bonds (and probably will have to be if I'm going to be sculpting). I can make the h bonds and make them real bonds for the sculpting, I'm just wondering of anyone has already done it or has a script around 2. When showing a cartoon of DNA the ribose ring in the backbone is always there no matter which setting you choose. How can I make the phosphates and the ribose rings show as a backbone cartoon tube and keep just the bases as filled sticks with rinngs? 3. Rings on DNA and RNA can be filled, in cartoon mode. But I can't get the rings to fill in on selected amino acids (H, W, Y, F) in a protein of that same file. Is there a fill amino acid ring setting? Thanks in advance for anything you can offer, Adam -- ___ H. Adam Steinberg Artist, Scientist http://adam.steinbergs.us Information Technology and Media Center Department of Biochemistry University of Wisconsin-Madison 433 Babcock Drive Madison, WI 53706 608/265-4982 ___ -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] error with the APBS plugin
Hello, I'm trying to use the APBS plugin to evaluate the electrostatic properties of my protein. On the one hand, I've have this error: Unable to assign parameters for the 1 atom in selection 'unassigned'. Please either remove thes unassigned atoms and re-start the calculation or fix their parameters in the generated PQR file and run the calculation using the modified PQR file (select 'Use another PQR' in 'Main') I tried to remove the selection but it seems that the atom in the selection has not been removed and I still obtain the same error message. Thus, I tried to edit the PQR file and I removed the atom in the PQR file but in this case I obtain a new error message: Reading PQR-format atom data from /home/Models/pymol-generated.pqr. Vio_ctor2: some error occurred. Vio_ctor: Vio_ctor2() failed. Problem opening virtual socket /home/Models/pymol-generated.pqr! Error reading molecules! ObjectMapLoadDXFile-Error: Unable to open file! could you explain the problem to me? thank you for your help, best regards, Anne L
[PyMOL] Second CCP4 workshop in USA, 1st announcement
We are pleased to announce that encouraged by last year's success we are again organizing CCP4 workshop at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found here http://www.ccp4.ac.uk/schools/APS-2009/ Title CCP4 school: From data collection to structure refinement and beyond Dates June 24 to July2 Site Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA First time this year There will be two days of beamtime available at GM/CA-CAT beamlines 23ID-B and 23ID-D for collecting data from participants' samples. The workshop content The workshop will feature authors and experts of many modern crystallographic software packages. It will be organized in three sections: lectures, tutorials and hands-on trouble-shooting. Note: There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Therefore, participants are encouraged to bring their problem data sets and/or crystals. Applicants Graduate students, postdoctoral researchers and young scientists are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection workshop and/or hands-on sessions. Application Application deadline is April 15. Selected participants will be notified no later than April 20. Application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2009/ Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT, Bld. 436, D007 Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov
