Re: [PyMOL] Mutagenesis tool failing on rotameric amino acids
Hi Carsten, Welcome and sorry for the delayed response, I was away at a training camp last week. Unfortunately, PyMOL cannot handle alternate conformations in the mutagenesis wizard. You can pick other atoms, but not those with alternate locations. Cheers -- Jason On Mon, May 17, 2010 at 8:39 AM, Carsten Siebenhaar csie...@gwdg.de wrote: Hello, I'm new to this board. I came across a certain problem with the mutagenesis tool. I got a pdb-file with amino acids that are partly displayed as 2 rotamers (so one amino acid displayed in two different ways in the Viewer). Usually, the mutagenesis tool works fine, but if you try to mutate this amino acid it won't accept it, but will just mention in the external GUI that it selected the corresponding atoms: You clicked /11//A/HIS`509/CD2`A Selector: selection sele defined with 20 atoms. PyMol keeps on asking me to pick a residue. Is there a way to easily avoid this problem or could this be considered a real bug? Thanks a lot! Carsten -- ___ 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 -- ___ 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] dihedral
Vivek, I know of no way to easily set a dihedral angle in PyMOL. We should consider making this easier in the future. Thanks, -- Jason On Sat, May 22, 2010 at 9:25 PM, Vivek Ranjan vran...@gmail.com wrote: Helllo, I am using pymol to change dihedral angles in a polymer chain. However, dihedral angles have poor precision. If I want to set them to, say 150, it never gets me that. I always get something like 149.5. I would like it to be 150.00. At least that precision. I was not able to find set_dihedral in the source code. Wondering if someone has some idea how a better precision can be achieved. Perhaps a tolerance issue that can be fixed easily. Please let me know. -- Thank you and Regards, Vivek Ranjan -- ___ 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 -- ___ 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] stick transparency
Hi all, Thanks a lot. It worked great. Cheers, Ariel On Sat, 2010-05-22 at 13:45 -0500, Jason Vertrees wrote: Hi all, Don't worry it's still there, just under a different command. Stick_color, stick_transparency, etc are properties of bonds, so it's best to now use 'set_bond' intead of 'set'. For example, set_bond stick_transparency, 0.5, objectName Cheers, -- Jason On Fri, May 21, 2010 at 3:13 PM, Michael Zimmermann micha...@iastate.edu wrote: Sorry, I didn't mention that I use 1.2r1 on xinXP It could be a version difference if the command does not work correctly for you. On Fri, May 21, 2010 at 11:50 AM, Ariel Talavera talav...@cim.sld.cu wrote: Hi again, Actually it seems that for some reason the comma after the value (0.5) invalidate the command line. Ariel On Fri, 2010-05-21 at 11:40 -0500, Matthew Franklin wrote: (I'm putting this back on-list) That's too bad. It worked for me: PyMOL 1.2r2, Windows XP. Can you set other properties of this object: color, stick_radius, etc.? - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly Company 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 -Original Message- From: Ariel Talavera [mailto:talav...@cim.sld.cu] Sent: Friday, May 21, 2010 12:26 PM To: Matthew Franklin Subject: RE: [PyMOL] stick transparency Thanks for the very quick answer, but it didn't succeed. Best, Ariel On Fri, 2010-05-21 at 11:18 -0500, Matthew Franklin wrote: Hi Ariel - Try set stick_transparency=0.5, peg_1 - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly Company 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 -Original Message- From: Ariel Talavera [mailto:talav...@cim.sld.cu] Sent: Friday, May 21, 2010 12:01 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] stick transparency Hi there, I am trying to set stick transparency using the following command: set stick_transparency, 0.5, peg_1, but with no success. The problem is with the selection, because if I use instead, set stick_transparency, 0.5, then every thing represented with stick get 50% transparent. Can you help with this? I am using Pymol 1.2 under Ubuntu 10.04. Thanks a lot in advanced, Best regards, Ariel Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you. -- ___ 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 -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University -- ___ 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-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] Jumping Frames
Hi All, I have written a quick little script to jump through various frames from an MD simulation loaded into PyMOL: ### from pymol import cmd import time def jump (*args, **kwargs): #Example: jump 1, 10, 20 #This will jump from frame 1 to frame 10 to frame 20 #for a total of 10 times (default) while pausing in #between frames for 0.1 seconds (default) #Example: jump 1, 50, 100, 1000, x=5, sleep=0.01 #This will jump from frame 1 to frame 10 to frame 100 to frame 1000 #for a total of 5 times while pausing in between frames for 0.01 seconds #Notice that I am using *args in order to allow a variable number of #frames to be specified x=10 sleep=0.1 for key in kwargs: if (key == x): x=kwargs[x] x=int(x) elif (key == sleep): sleep=kwargs[sleep] sleep=float(sleep) else: continue args=list(args) for i in range (x): #This loop runs through all of the selected frames x times #Need some way to recognize input from user to exit loop/return for j in range (len(args)): #This loop runs through each of the selected frames one time #Need some way to recognize input from user to exit loop/return cmd.frame(int(args[j])) #This skips to the specified frame cmd.refresh() #This refreshes the display time.sleep(sleep) #This pauses the loop for a period of time, acts like frame rate return cmd.extend(jump, jump) # I have two questions: 1) Is there some way that I can tell PyMOL to exit either of the for loops by pressing the keyboard/stdin? The purpose of jumping through various frames is to look for conformational changes in the structure but with the current script, it is necessary to run through both for loops before it stops. However, I would like a way to stop the script at any time by simply pressing a user defined button on the keyboard. I've marked the places above where the script would be required to look for user input and move on if no input is provided. Alternatively, I could have the user hold down a keyboard key in order to run through the loops and once the key is released have it automatically exit/return. Either would be fine. FYI, I did try to play with raw_input command but it didn't seem to work/help. 2) In this case, since I'm using *args and **kwargs, how do I specify the usage? Right now, when I do jump ? in PyMOL, it just spits out Usage: jump without any of the usual usage information. Is there some explicit way of telling PyMOL exactly what usage information to print out?? Any suggestions would be greatly appreciated! Thanks. Sean _ MSN Dating: Find someone special. Start now. http://go.microsoft.com/?linkid=9729707-- ___ 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] Mutagenesis tool failing on rotameric amino acids
Dear Carsten, On 17 May 2010 14:39, Carsten Siebenhaar csie...@gwdg.de wrote: Hello, I'm new to this board. I came across a certain problem with the mutagenesis tool. I got a pdb-file with amino acids that are partly displayed as 2 rotamers (so one amino acid displayed in two different ways in the Viewer). Usually, the mutagenesis tool works fine, but if you try to mutate this amino acid it won't accept it, but will just mention in the external GUI that it selected the corresponding atoms: You clicked /11//A/HIS`509/CD2`A Selector: selection sele defined with 20 atoms. PyMol keeps on asking me to pick a residue. Is there a way to easily avoid this problem or could this be considered a real bug? Thanks a lot! Carsten Do you want to retain the double conformations? If not, then you could use PyMOL to delete the alternate conformations thus, just retaining one of them. # select remove all non A altlocs remove not (alt ''+A) # reset the PDB information alter all, alt='' taken from: http://pymolwiki.org/index.php/Property_Selectors#Alternate_Locations I hope this helps. Folmer Fredslund -- ___ 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-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
