[PyMOL] side chain helper glycine

Hi there, I used the side chain helper option to create a binding site in the protein. However I want include a glycine, which doesn't show up. Even when I create an extra object with the glycine and an neighbouring residue I didn't get the carbonyl oxygen atom of glycine and I don't want to s

[PyMOL] specify size and dpi and automatic adjustment of pixels?

kep the aspect ratio. E.G. could pymol than automatically reduce the pixelsize or increase it? Best Regards Christian -- Christian Roth Strukturanalytik von Biopolymeren Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Email christian.r...@bbz.uni

[PyMOL] APBS Tools library error

It works. This was a centos45 version of pymol. Does anyone has encountered a similar error and found a more elegant solution than just using an old pymol for such calculations? Thank you very much in advance for your help an suggestions. Best Regards Christian -- Christian Roth Inst

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

> Also I've found the same software- pose view (in that article > >>> > >>>I've also > >>> > >>> > found link on it). Its very friendly but I've noticed some erorrs > >>> > >>>during &g

[PyMOL] Visualisation of protein-ligand interactions in pymol

Hi James, LigPlot is free for academic users. You just have to verify that you are a academic user. MOE does a simimlar representiation but is definitely not free. Christian -- Live Security Virtual Conference Exclusi

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

Hi James, the program you can use for this is ligplot from Roman Laskowski at the EBI. the solvent accessability shading is done with the help of naccess. Best Regards Christian Am Dienstag 26 Juni 2012 08:07:07 schrieben Sie: > By the way > > in some papers I've seen 2D schematic diagrams

[PyMOL] clipping planes

Dear all, it is nice to set via mouse wheel the clipping. Is it possible to get this values somewhere out of pymol that one could use the actual values in a script? I find it a bit complicated and time consuming to play always a few times with the values in a script, to find values which looks

[PyMOL] pymol castp mesh surface representation

Dear all, I used Castp for a pocket analysis. If i displax a mesh I have a continous representation. If I use surface representation just parts are displayed, probably as a result that just parts of the aminoacids are used to define the pocket, I guess. Is it possible to create a surface like

[PyMOL] font list

Hi, ist there a list of example letters for the availbale fonts in pymol? It would be nice to see which font may produce a more italic like expression or which a more roman or Arial like font. Thanks and Best wishes Christian --

[PyMOL] label position

Dear all, I want label a few distances independently with my own labels. I set a label in the form label /wt//A/THR`254/CA, "10.0"+ u"\u00c5".encode('utf-8') which I can move independently using the set label positio command. If I incorporate a second label and try to change the position with t

[PyMOL] rotate translate two different objects indpendently and legend

Dear all, I have a two chain protein and I want translat and rotate it using the commands translate and rotate. It is complicate to choose the rigth angel, because I cannot see the rotation axis. Is there a way to draw the axis system for the objects to see around which axis and how much I must

[PyMOL] pymol and bonds to symmetry related molecules

Dear all, I have incorporated a bond to a symmetry related molecule in my structure and I want see this bond in my picture. Is it possible to visualize this bond in pymol? Thansk in advance for your help. Christian -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch