[PyMOL] Fw: symmetry and pdb remark

mate arrangement, as in the remark added PDB for 2zan fitted to 2zam? Why after pymol alignment, the same remark information leads to different mates arrangement? I am looking forward to getting a reply from you. Smith Forwarding messages From: "Smith Liu"

[PyMOL] symmetry and pdb remark

Dear All, I have a symmetry problem, which I hope I can get your help. For both PDB 2zan and 2zam, they are for the same protein, they conformation were similar except that 2zam was apo and 2zam was ATP binding. 2zaz was got by soaking the 2zam crystal with ATP. Both were P65 space group

[PyMOL] on the generate symmetry mates function

Dear All, Once load a pdb with space group P 65 by pymol, I click action then generate symmetry mates within 4 A, I find in the pymol windows, there were 7 molecules displayed (one was the original pdb) . Here I want to ask, in the 7 molecules displayed, all the other 6 molecules were really t

[PyMOL] a special phenomenon on using pymol

Dear All, Today as every day I do, I align 2 pdb files by pymol. After a moment, I find the aligned 2 molecules start to rock back and forth continuously in the pymol window (from about 45 degree to -45 degree). Today I never used the rotate or rock command. Will you please explain why this

[PyMOL] on the alignment command

Dear All, Suppose my protein A PDB contains chian A, B, C, D, and my protein B PDB contains chain E, F, G, H, I want to align all protein A without chain D, with all protein B without chain H, will you please tell me the align command? Smith

[PyMOL] on contact surface and domain angle

Dear All, Will you please tell me the command to calculate the contact surface area between 2 sub-units in the protein complex? Will you please also tell me the command to calculate the angle in degree between 2 domains in a sub-unit? Smith ---

[PyMOL] calculation of the contact surface between subunits

Dear All, Will you please tell me the pymol command for calculation of the contact surface between subunits of a protein complex? And what is the command for calculation of the cavity volume surrounded by the protein complex? Smith--

[PyMOL] how to close displaying a molecule

Dear All, Suppose by pymol I have opened A.pdb abd B.pdb. Is anyway I close B.pdb and have only A.pdb displayed? Smith -- ___ PyMOL-users mailing list (PyMOL-users@lists.sou

[PyMOL] Fw: on load new B-factors

Forwarding messages From: "Smith Liu" Date: 2015-12-10 22:27:03 To: "pymol-users@lists.sourceforge.net" Subject: [PyMOL] on load new B-factors Dear All, When I use "loadBfacts mol, [startaa, [source, [visual Y/N]]]", I meet the followi

[PyMOL] on load new B-factors

Dear All, When I use "loadBfacts mol, [startaa, [source, [visual Y/N]]]", I meet the following error message, "File "Some_directory\parse.py", line 250, in parse self.result=app(layer.kw[0],layer.args,layer.kw_args) File "loadBfacts.py",line 16, in loadBfacts obj=cmd.get_object_list(mol)[0] Ty

[PyMOL] color based on residue sequence

Dear All, Is any way by pymol we color the protein based on residue sequence, for example from red starting resi 1 gradually to blue at residue 1000? Smith-- Go from Idea to Many App Stores Faster with Intel(R) XDK Giv

[PyMOL] how to separate the complex subunits

Dear All, Suppose I have a protein complex displayed by pymol, is any way pymol can separate its subunits in a fixed and beautiful patten of arrangement in the pymol window? If the subunit contains may alpha helices too dense for display each helix visibly by pymol, is any way pymol can exte

Re: [PyMOL] save_transformed.py

>https://sourceforge.net/p/pymol/mailman/message/27824450/ > >Hope that helps. > >Cheers, > Thomas > >On 28 Nov 2015, at 02:52, Jordan Willis wrote: > >> Yes, but what you are describing, saving a new view is your purpose. All >> orient does is move the camer

[PyMOL] on axis of the subunit

Dear All, Will you please show me how to display an axis of a subunit or a domain by pymol? Smith-- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page

Re: [PyMOL] save_transformed.py

n load it. You can’t code a view change within the PDB. On Nov 27, 2015, at 11:27 PM, Smith Liu wrote: Dear Jordan, My purpose is, once you move a molecule in pymol, I want to save a new pdb, when we open the new pdb, pymol will display the new position as default. The script

Re: [PyMOL] save_transformed.py

p/Transform_selection there is another script. I do not know how to use this scripts to realize my purpose. Smith At 2015-11-28 15:07:18, "Jordan Willis" wrote: very possible, can you send me the script? On Nov 27, 2015, at 10:58 PM, Smith Liu wrote: By Jordan, by

[PyMOL] save_transformed.py

.pdb” On Nov 27, 2015, at 9:08 PM, Smith Liu wrote: Dear All, Osvaldo is new here for this question, so I repeat it a little. By pymol I open a pdb and orient it and I want to save the oriented pdb. First I input command "orient" after load the pdb, then I input comman

Re: [PyMOL] on PDB

d on your operating system and architecture. Shane Shane Caldwell McGill University On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu wrote: Dear All， Once a molecule displayed in pymol, first I input command "orient", then I input command "run save_trannsforme.py all, newpd

Re: [PyMOL] on PDB

pt defines a new command which can be run e.g. `save_transformed , `. You don't have to replace anything in the script yourself. Note that the save_transformed command modifies the object it's run on, so you might want to run it on a backup copy by first calling `create _backup, `

Re: [PyMOL] on PDB

.pdb? Ortherwise how to get the output modified PDB? I am looking forward to getting a reply from you. Smith At 2015-11-26 14:24:15, "Andreas Forster" wrote: http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures Andreas On Thu, Nov 26, 201

Re: [PyMOL] on PDB

ater use. The output set_view command will return the window to the same camera settings Shane Shane Caldwell McGill University On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu wrote: Dear All, Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can sav

[PyMOL] on PDB

Dear All, Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented? Smith-- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amaz

[PyMOL] on save_transformed.py

Dear All, In http://pymolwiki.org/index.php/Modeling_and_Editing_Structures there is "save_transformed.py". Will you please show me how to use this script? There is no problem to do "run save_transformed.py". But after click that command, how to get and save the transformed pdb file? Smith-

[PyMOL] on PDB display and calculation

Dear All, Once I have displayed a tetramer PDB by pymol, is any way I can get the central axis of the tetramer and display it? Is any way I can get the cross-section of the tetramer (perpendicular to the central axis) and display it? If the tetramer is asymmetric, then how to get the central a

[PyMOL] on async

Dear All, Will you please tell me the meaning of "async"in pymol script? Smith-- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sour

[PyMOL] what is wrong on my using centroid.py

Dear All, When I run the centroid.py, I have the following error message: "NameError: global name 'move' is not defined". My centroid.py script downloaded (have I misdone or miseddited something?) is as following. Will you please tell me how to solve the error message issue? Smith --- Se

[PyMOL] on using pymol scripts

Dear All, If I want to use a pymol script, for example the script on centroid, will you please tell me how to download the corresponding script from the pymol website? Smith-- __

Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

n Wed, Nov 18, 2015 at 7:49 AM, Smith Liu wrote: Dear All, Is any way we can colour the molecule by pymol based on the y values in the z y z coordinates, so that we can view easily the residues (or atoms) with equivalent position in the primary sequence but has a y-axis shift in the 3-D

[PyMOL] on coloring residues based on y values in the x y z coordinates

Dear All, Is any way we can colour the molecule by pymol based on the y values in the z y z coordinates, so that we can view easily the residues (or atoms) with equivalent position in the primary sequence but has a y-axis shift in the 3-D structure? Smith

[PyMOL] on coloring residues based on residue conservation

Dear All， Is any simple method by pymol we can color residues based on the residue conservation? Best regards. Smith-- Presto, an open source distributed SQL query engine for big data, initially developed by Facebook

[PyMOL] volume measurement

Dear All, If there is a cleft (looks like letter "C", which is not totally closed) formed by 2 subunits, will you please tell me by pymol how to measure the volume of the cleft formed? Best regards. Smith--

[PyMOL] on cartoon representation

Dear All, Recently I have noticed in Science and Nature paper, the author present the helix in cartoon as thin as that observed in VMD (and even similar in appearance). I do not know whether the author made the image by pymol or by VMD. Is any way for pymol to make helix in carton as observe

[PyMOL] on surface function in the setting

Dear All， For my windows version of pymol, I cannot locate the surface function under the setting button. Will you please tell me how can I make my surface cavity pocket function workable? Best regards. Smith--

[PyMOL] on cylindrical helix presentation

Dear All, Suppose a protein contains 2 subunits. Will you please introduce to me by pymol how to represent helix in one subunit as cylindrical helix, and helix in another subunit as regular helix? Best regards. Smith---

[PyMOL] a command related to pymol "show as"

Dear All, Will you please tell me how to process so that a long helix will be shown as a long rod (pr long bar） by pymol? Best regards. Smith-- ___ PyMOL-users mailing list

Re: [PyMOL] secondary structure disappears

I think the secondary structure record (SS) has been lost during your splitting. So just add and edit the SS record in the PDB file to the lost ones. Smith At 2015-07-23 22:23:24, "H. Adam Steinberg" wrote: Hi All, If you fetch 3ow9 in PyMOL, split_states to get all six of the strands,

Re: [PyMOL] how to measure the distance of 2 hydrophobic residues

something more complex? Could you provide more details about your problem? Cheers, Osvaldo. On Wed, Jul 8, 2015 at 12:33 PM, Smith Liu wrote: Dear All, Pymol has the function to measure the distance betweeen 2 atoms. In addition, if 2 hydrophobic residues are close enough, there will be h

[PyMOL] how to measure the distance of 2 hydrophobic residues

Dear All, Pymol has the function to measure the distance betweeen 2 atoms. In addition, if 2 hydrophobic residues are close enough, there will be hydrophobic interactions betweem them. But will you please tell me how to measure the distance between 2 hydrophobic residues by pymol? Best regar

[PyMOL] on color based on b-factor spectrum

Dear All, in the pymol default color based on b-factor spectrum, will you please tell me how pymol determines the specific color based on the b-factor leve? For example, in which scope of b-factors the protein part would be in red and in which scope of b-factors the protein part would be in gr