Re: [PyMOL] center at x,y,z

On 9/18/06, Björn Kauppi wrote: Hi all, How do I center at a specific coordinate? Can not find any obvious way, by searching the web and manuals. middle clicking on an atom given at those coordinates should work. Isn't that what you want? HTH Ramesh

Re: [PyMOL] A suggestion

ite seamless. Only hitch (and that is not the right word) is that if you want to effect a bond rotation or something on a pose, you can't do it since this is a multi-state object. Hope this helps. Do let me know if you have problem with this. best wishes Ramesh Sistla

Re: [PyMOL] Manually move one molecule relative to another

S. Frank Yan wrote: Hi all, I was wondering if there's a way to manually move a molecule relative to other molecules (such as in the case of manual docking) using the mouse. I searched the previous posts and found that MovF/RotF are the way to do that. But, when using these mouse functions to m

[PyMOL] lipophilic surface

Hi List! Is it possible to generate a molecular surface with lipophilic potentials mapped on to the surface? I guess there is nothing in pymol as yet to do this directly. Is there any work around? Best regards -- :-) Ramesh K. Sistla May the wicked become good, may the good attain peace May

Re: [PyMOL] fit command

Andrea Spitaleri wrote: Thanks, it worked. So why fit did fail in doing that? Well, I will leave it to some experts. I did spend sometime trying to understand that, but couldn't. I am still learning pymol!:)) -- :-) Ramesh K. Sistla May the wicked become good, may the good attain peace M

Re: [PyMOL] fit command

Andrea Spitaleri wrote: Hi all, i have got two pdb files, ref.pdb and docked.pdb, where ref.pdb contains the protein A and docked.pdb the protein A + a docked ligand. when I try to run fit ref, docked I get: ExecutiveRMS-Error: No atoms selected. I tried to select the atoms or create a new object

Re: [PyMOL] labelling using single letter codes

andr...@biochem.utah.edu wrote: Hey Ramesh, for all sorts of labeling, image manipulation programs like photoshop or the gimp are superior. Convince yourself how simple it is even to adjust the z position of the label in a stereo picture by moving it (one partner of the stereo pair) horizontall

Re: [PyMOL] labelling using single letter codes

Ezequiel H Panepucci wrote: Hello Ramesh, use: label n. ca, one_letter[resn] Cheers, Zac Thanks Zac. that was indeed very useful. But I have one more problem. Doing thus gives me only the name of the aa, not its number. How to give the label command in order to give the number

[PyMOL] labelling using single letter codes

Hi List! Is it possible to do the labelling using single letter codes for the amino acid residues rather than the three letter codes? Regards -- :-) Ramesh K. Sistla May the wicked become good, may the good attain peace May the peaceful be freed from bonds, may the freed set others free

Re: [PyMOL] "draw" command

Warren DeLano wrote: PyMOL Testers: 0.99beta07 also contains a new command: "draw" which creates an oversized OpenGL image using the current window. Is this version not available yet for linux? I could find only 0.99beta_02. -- :-) Ramesh K. Sistla May the wicked become good, may the good a

Re: [PyMOL] the conserved residues can be overlapped?

Sabuj Pattanayek wrote: > Hi, > > I was trying to find information online/and in the archives of the > mailing list to do what you are asking. You can try "help fit" which > will give you some more commands to try. You can also try "help > pair_fit". Unfortunately I know I'm doing something wrong

[PyMOL] transparent(better) gives error!

Hi List! When i try to set Action > Preset > ligand_sites > transparent(better) for any protein, I get the following error: Traceback (most recent call last): File "/soft/pymol/modules/pymol/parser.py", line 255, in parse exec(com2[nest]+"\n",pymol_names,pymol_names) File "",

[PyMOL] pymol crash!

Dear List! I grabbed 0.96and installed. It is a beauty. Only that when I clicked on getview button, it copied the matrix to clipboard and crashed. The error it returned is: PyMOL: Viewing matrix copied to clipboard. unable to alloc 1869182081d bytes /usr//bin/pymol: line 14: 24056 Aborted

[PyMOL] polar surface area with pymol

Hi List! Is there any way I can calculate the PSA of a molecule with pymol? Will be grateful for any hints. Thanks and regards, -- Ramesh Sistla Science Fellow This email and its attachments are confidential and proprietary to AURIGENE Discovery Technologies and are meant for the intended