Re: [PyMOL] Moveable Camera

Hi Mike, Tom, > If I'm not mistaken, it is always the camera that is moving when you rotate > a molecule. Unfortunately I have to inform you that you are mistaken... In Pymol the camera is always fixed. That also means that it is not possible to have the camera fly through the protein. But there

[PyMOL] msms_pymol.py

Hi All, When I run the script download from http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/, I issue the commond: calc_msms_area 2mlt-melittin, there are always something wrong as follows: CmdLoad: "D:/singapore-NTU/HU/modelling/2MLT-melittin.pdb" loaded as "2MLT-melittin". PyMOL>run C:/Prog

Re: [PyMOL] Moveable Camera

Dear Tom, If I'm not mistaken, it is always the camera that is moving when you rotate a molecule. That is how Pymol is so fast - only one point is actually moving. Have you investigated the mset command to set waypoints for the camera? http://pymolwiki.org/index.php/Mset http://pymolwiki

[PyMOL] Moveable Camera

Hello everyone, I am trying to do something that seems a little uncommon. I wish to have a moveable camera. So instead of rotating/translating the protein/molecule/DNA I move the camera point/location and the vector that the camera points in. I wish to be able to move into the molecule and view

Re: [PyMOL] list of hydrogen bonds

Hi Jason, is it possible to print out a list of hydrogen bonds found by polar contacts. Maia -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: htt

Re: [PyMOL] PyMOL-users Digest, Vol 48, Issue 6

or, you can simply write the coordinates to a file in PDB format and load it in PyMOL. According to my experience, this way is more flexible and you can manipulate the cloud easily. For example, you can change the color of the cloud, or show it as spheres of different radii. But for a cgo, you

Re: [PyMOL] msms_pymol.py

Hi, sujuan, Robert provides a rich collection of pymol plugins. I myself benefit a lot from the collection. For using msms, you can have a try of my alternative to Robert's msms_pymol.py at: http://www.biotec.tu-dresden.de/~hongboz/pymol_script/msms_pymol.py It has a graphical user interface.

Re: [PyMOL] how to use side chain helper only on some residues, but not on other residues in the same session

Hi Maia, Just turn on the setting for one of the proteins instead of globally. If you type the following, set cartoon_side_chain_helper, on it will turn it on for all objects. So, try this instead set cartoon_side_chain_helper, on, protein1 Here's an example: # fetch two proteins, 1cll and

Re: [PyMOL] how to use side chain helper only on some residues, but not on other residues in the same session

Hi, I want to use a command to show some main chain atoms (that make hydrogen bonds with my ligand), but not all of them. When I use side chain helper, it hides all main chain atoms for different objects, no matter where I put the command, between the objects in the script etc.Is there a way t

Re: [PyMOL] msms_pymol.py

Hi Sujuan, On Tue, 11 May 2010 14:38:52 +0800 sujuan wang wrote: > Hi All, > When i run the script download from > http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/, I issue the commond: > calc_msms_area 2mlt-melittin, there are always something wrong as follows: In addition to my previous

Re: [PyMOL] msms_pymol.py

Hi Sujuan, Given that this is my script, I'll answer. :) On Tue, 11 May 2010 14:38:52 +0800 sujuan wang wrote: > Hi All, > When i run the script download from > http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/, I issue the commond: > calc_msms_area 2mlt-melittin, there are always something

Re: [PyMOL] drawing a cloud of points?

Hi Jose, Depending on the number of points you could (1) create CGO objects for each; (2) use the pseudoatom command supplying the "pos" parameter for each particle. For more info check out http://www.pymolwiki.org/index.php/Pseudoatom and http://pymol.sourceforge.net/newman/user/S0500cgo.html fo

[PyMOL] msms_pymol.py

Hi All, When i run the script download from http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/, I issue the commond: calc_msms_area 2mlt-melittin, there are always something wrong as follows: CmdLoad: "D:/singapore-NTU/HU/modelling/2MLT-melittin.pdb" loaded as "2MLT-melittin". PyMOL>run C:/Prog

Re: [PyMOL] PyMOL-users Digest, Vol 48, Issue 5

Dear Sabuj, thank you for your reply. Unfortunately, I do not have the 3 pin mini din cable (in Europe and Asia is not included in the 3D Vision kit). However, I have finally been successful! The problem was that in order to find the correct Nvidia driver settings, I changed the settings and