Re: [PyMOL] PyTMs

Hej Raag, my name is Andreas and I wrote PyTMs back for my PhD. It essentially uses PyMOLs basic editing functions to build PTMs onto protein models. PyTMs is a simple tool and has its clear restrictions, but generally it is nice to play around with and explore hypotheses with. The challenge is

Re: [PyMOL] Detecting holes/cavities in surface

I haven't used it before, but I there is a PyMOL plugin called KVfinder that detects cavities. Potentially this offers an approach for you. On Jul 20, 2016 12:05 AM, "Daniel James" wrote: > Hi all, > > I haven't used this list before but can't find an answer to my

Re: [PyMOL] Selective valency on bond

The easiest way to deal with this is setting the valence or valence_mode individually for the object. set valence, 0, object1 set valence, 1, object2 Cheers, Andreas On Mon, Jun 13, 2016 at 11:56 AM, McIntyre, Patrick wrote: > Dear PyMol users, > > I have a crystal

[PyMOL] Electrostatic Map for a molecule containing a citrulline

Dear all, a colleague is interested in generating an electrostatic map of a protein containing a citrulline. Does anybody have any experience with this and could recommend any approach? Cheers, Andreas -- Site24x7 APM

Re: [PyMOL] Pymol for inorganic chemists - dealing with bonds

Hej Henrique, not an inorganic chemist here, but some suggestions anyway: Metallic centers should be displayable as spheres using the *show*, or *show_as spheres* commands. The radius can be altered using: *set sphere_scale, value, selection* The bonds are more problematic. Pymol has some

Re: [PyMOL] Viewing Electrostatic Potential maps for multimeric complexes

You could try to split the states and subunits in PyMOL, then save them as individual .pdb's and then use those to generate multuple .dx files. On Jun 8, 2015 2:38 AM, Rahul Sheth chaav...@gmail.com wrote: Hello, I am new to using PyMol. I wanted to see the electrostatic potential map for a

Re: [PyMOL] Printing Protein Surface residues

sequentually, but usually one doesn't care for the heteroatoms. This is just to avoid potential influences by surrounding waters, or other stuff. Cheers, Andreas On Thu, May 21, 2015 at 1:27 PM, Andreas Warnecke 4ndreas.warne...@gmail.com wrote: Hej, depends on what you want, single

Re: [PyMOL] Printing Protein Surface residues

Hej, depends on what you want, single atoms or residues. You can output the available surface are for every atom and then decide which ones are accessible based on your cutoff stringency. Here is some code that will print the info in PyMOL, alternatively you could modify it to print to a file

Re: [PyMOL] Pymol wiki search is not working

Hej, While its not perfect I usually end up using google search and adding 'pymol wiki' to the search terms. Works for me. Cheers, Andreas On Feb 4, 2015 2:50 PM, Matthew Baumgartner mp...@pitt.edu wrote: Yes, I've been having this problem for a while. I contacted Jason Vertrees about it a

Re: [PyMOL] Phosphoserine

Hi Monica, You can check out the plugin PyTMs, which allows you to introduce PTMs into protein models within PyMOL: http://www.pymolwiki.org/index.php/Pytms Let me know should you need any assistance with this plugin. Cheers, Andreas On Fri, Jan 30, 2015 at 4:59 PM, Monica Mittal

Re: [PyMOL] ray trace mode 1 playing up pymol 1.7.4?

Hi, This may also be related to the setting: ray_trace_mode Try: set ray_trace_mode, 0 This will deactivate outlines (ray_trace_color) during ray tracing. The wiki page has some examples. Cheers, Andreas On Dec 16, 2014 6:05 PM, H. Adam Steinberg h.adam.steinb...@gmail.com wrote: The

Re: [PyMOL] selection of a set of amino acids

Hi, There is a script available on the pymol wiki called zero_residues. This will allow you to easily renumber any AA sequence. As far as other heteroatoms are concerned you could consider removing them (remove hetatm), or extract them into a second object. Another alternative is to simply adjust

Re: [PyMOL] Goodsell colouring

Hi Jacob, I'm not familiar with goodsell, but some selection algebra should be a solution: Try something like: util.cbaw # color by atom (white carbons) color grey80, chain B and elem C color grey70, chain C and elem C #... etc. There are also pymol wiki pages for coloring and selection algebra

Re: [PyMOL] set size nb_spheres

Hi Erica, I prefer to leave the vdw value untouched, as this may affect operations that rely on this value. Instead you can alter the sphere scale: set sphere_scale, value, selection e.g.: set sphere_scale, 1.5, hetatm show_as spheres will increase the sphere scale of heteroatoms (i.e.

Re: [PyMOL] How to build imedazole by using builder

Hi Surya, Using the interactive builder is usually the way to go. To get you started you may need a starting atom, which you could create using the pseudoatom command: http://www.pymolwiki.org/index.php/Pseudoatom Note that the builder has some templates, e.g. the cyclopendadiene that you can

Re: [PyMOL] CONECT table

Hi, It appears that the following: Select gluco, bound_to resn NDG Show sticks, gluco does not work. I'm not sure if the glycosylation is handled as a separate residue, but you could try: select glucoasp, byres (neighbor (resn NDG)) show sticks, glucoasp FYI: There are pages on selection

Re: [PyMOL] CONECT table

Oh, and it should be glucoasn, of course. :-P On Oct 8, 2014 1:26 AM, Andreas Warnecke 4ndreas.warne...@gmail.com wrote: Hi, It appears that the following: Select gluco, bound_to resn NDG Show sticks, gluco does not work. I'm not sure if the glycosylation is handled as a separate residue

[PyMOL] Testing for incentive vs. open-source in scripts

Dear PyMOL users, I am wondering if there is any way of testing whether a PyMOL version is open-source or incentive for use in scripts. I'm thinking of something similar to 'cmd.get_version()'. The reason for this is that I am e.g. using the 'alter' command on custom properties in scripts, which

Re: [PyMOL] Testing for incentive vs. open-source in scripts

to the version. I don't know where that is stored from the top of my head. Maybe Thomas knows. Cheers, Tsjerk On Fri, Oct 3, 2014 at 2:09 PM, Andreas Warnecke 4ndreas.warne...@gmail.com mailto:4ndreas.warne...@gmail.com wrote: Hi, Thanks for the reply. I'm just having

Re: [PyMOL] Testing for incentive vs. open-source in scripts

this, or not? On 10/3/14 3:06 PM, Andreas Warnecke wrote: Hi all, just to specify the issue: the problem is not the crash, because the script continues due to the try statement. The issue is that PyMOL handles and prints the exception from the 'alter' command into the console. I would like to avoid

Re: [PyMOL] drawing arows, CONE cgo doesn't work.

Hej, if you simply copy-paste the wiki entry into PyMOL you will get the error. This code is intended to be run as a block (e.g. from script) and creates e.g. problems with indentation, or other errors. A simple solution would be to wrap the commands to a block using python and python end.

Re: [PyMOL] Coloring of helices

Hej, you can try to exclude the backbone from your selections using not: select V27, (resi 27 and EXA) and not (name N+C+O) # I included the CA in this selection etc. This should select the residue atoms excluding the backbone (except CA). If you have hydrogens in the structure you may need

Re: [PyMOL] Hbonds in grid mode

Hej, The reason for this happening is that the distances are a separate object. What you are looking for is grid_slot. Simply assign the distance and protein objects to the same slot. http://www.pymolwiki.org/index.php/Grid_mode http://www.pymolwiki.org/index.php/Grid_slot Cheers, Andreas On

Re: [PyMOL] directing output of print

Hej Harry, This PyMOL wiki page may help you out further, it may be hard to find without the underscore in the name: http://www.pymolwiki.org/index.php/Get_Area If you use the load_b=1 option, PyMOL will overwrite the b-factor. You could select the atom by the overwritten b-factor, e.g.: select

Re: [PyMOL] Fwd: color by RMSF or RMSD

Hej Nidhi, I'm not familiar with the two scipts but the usage appears correct. You can check the arguments in PyMOL using e.g.: rmsf_states ? and/or: help rmsf_states I assume the color_b command is a simplification of the spectrum command, so you could also check out:

Re: [PyMOL] How to show atom index or atom serial when clicking on an atom?

Hej Jose, This script may do what you need. The core is to use iterate over the different identifiers. I'm not sure if there's a more convenient way, though. python def get_macro_name(sele): ''' will return

[PyMOL] Fwd: Re: How to show atom index or atom serial when clicking on an atom?

-- Forwarded message -- From: Andreas Warnecke 4ndreas.warne...@gmail.com Date: Jul 14, 2014 1:03 AM Subject: Re: [PyMOL] How to show atom index or atom serial when clicking on an atom? To: Jose Borreguero borregu...@gmail.com Cc: minor amendment, changin the iterate line

Re: [PyMOL] side chain helper glycine

Hej, I'm not sure about the side chain helper options, but you can always selectively show displays. You could try something like: show_as cartoon, object show sticks, sele and not name N+C+O or: show_as cartoon, object show sticks, sele hide sticks, name N+C+O Either option should show the

Re: [PyMOL] Set fullscreen and grid mode in batch script

Hej, I haven't tested, but the grid_mode should work, all you need to do is correct the underscore typo: set grid_mode, 1 # without _ set grid_slot, 2, object2 set grid_slot, 1, object1 Picture size and quality is not controlled by viewport unless you are making a movie, in that case set

Re: [PyMOL] command question RE printing out distances to text file

Hej Suzanne, you will need to append the other two distances to the script to get them printed. Following your example that would be something like: # calculate the distance and store it in dst dst1=cmd.distance('tmp','B///297/cb','A///17-19/cb')

Re: [PyMOL] command question RE printing out distances to text file

, Andreas Warnecke 4ndreas.warne...@gmail.com wrote: Hej Suzanne, you will need to append the other two distances to the script to get them printed. Following your example that would be something like: # calculate the distance and store it in dst dst1=cmd.distance('tmp','B///297/cb','A///17-19