[PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

Hi, Pymol-users I have my protein shown as cartoon and colored with spectrum. Now I would like to show several residues at different places with sticks representation. when I tried, I can not get the color consistent between the backbone CA and the carbons on the sidechain. I searched the arch

Re: [PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

: Thursday, May 21, 2020 9:19 AM To: Chen, Qiang ; pymol-users@lists.sourceforge.net Subject: RE: Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring Hi Charles, This pml script does want you want, # Color the carvons atoms of the sidechain the same as the color

Re: [PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

I tried that. that is actually how I found this is a way to color them according the CA color assigned in the spectrum. Charles From: Olson, Linda Sent: Thursday, May 21, 2020 12:24 PM To: Chen, Qiang Subject: Re: Consistent coloring between sticks of

Re: [PyMOL] renumber (Oganesyan, Vaheh)

Coot is also an option. CCP4 is much better/flexible though. > On Jun 15, 2020, at 3:57 PM, pymol-users-requ...@lists.sourceforge.net wrote: > > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit

[PyMOL] hydrogen bond list for a series of files

Hi, Pymol users Could you help me do this in an efficient way? Let me describe the task I try to do. I have a series of numerically ordered files, say model00.pdb model.01.pdb …… model.30.pdb All the pdb have the same protein composition, chain A, B, C, D, and E. Their relative position is di

Re: [PyMOL] hydrogen bond list for a series of files

his simple thing does not work. Any suggestion? Thanks! Charles From: Mooers, Blaine H.M. (HSC) Sent: Monday, June 15, 2020 9:44 PM To: Chen, Qiang ; pymol-users@lists.sourceforge.net Subject: RE: hydrogen bond list for a series of files Hi Charles, Make sure th

Re: [PyMOL] hydrogen bond list for a series of files

Hi, Blaine, Then the question becomes how to generate a list with 30 or 300 numbers. Will this work? file_list=list(range(00, 30)) Thanks! Charles From: Mooers, Blaine H.M. (HSC) Sent: Tuesday, June 16, 2020 9:57 AM To: Chen, Qiang ; pymol-users

Re: [PyMOL] hydrogen bond list for a series of files

Great, thanks! Really appreciate your help! Charles From: Mooers, Blaine H.M. (HSC) Sent: Tuesday, June 16, 2020 10:51 AM To: Chen, Qiang ; pymol-users@lists.sourceforge.net Subject: RE: hydrogen bond list for a series of files Hi Charlie, This will give the

[PyMOL] hydrogen bond list for a series of files

afad308d812081e49%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637279173371378327&sdata=v28nxT%2ByGrbeZCuvUvBY327R7wDd2z%2FSDo13H8%2BoPwc%3D&reserved=0 or, via email, send a message with subject or body 'help' to pymol-users-requ...@lists.sourceforge.net You ca

[PyMOL] color by index

Will spectrum just works for your purpose? spectrum count, blue red, yourprotein, byres=1 you can switch off byres if you really want color by atom index. Charles > hello everyone! > I am trying to color an explicit distribution by color (say blue to red) > pls help me with the command color

[PyMOL] choice of color in util.cbc

Hi, Pymol Users Is it possible to choose different color pattern when using util.cbc? Wiki says I could use the following to choose the first_color util.cbc 6uwz, first_color=1, quiet=0 6uwz is just an example of a pentameric protein. However, there is no change when specify any other number f

Re: [PyMOL] choice of color in util.cbc

Thanks! This works well. "Spectrum chain" is more flexible and powerful in this case. Charles From: Thomas Holder Sent: Tuesday, July 14, 2020 2:24 PM To: Chen, Qiang Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] choice of color in ut

[PyMOL] transform an channel pore profile

Hi, Pymol users, Would anyone help me to transform the calculated pore profile along with the protein. I have a couple of proteins and I calculated the pore profiles using MOLE. I downloaded the pymol scripts to regenerate the pores with the protein. when I aligned these proteins, the pore app

Re: [PyMOL] transform an channel pore profile

I got the answer. Actually, the solution is so simple, matrix_copy. Charles From: Chen, Qiang Sent: Friday, July 24, 2020 12:46 PM To: pymol-users@lists.sourceforge.net Subject: transform an channel pore profile Hi, Pymol users, Would anyone help me to

[PyMOL] Salt bridges in same chains

Hi, All, I am writing a script to find all salt bridges in a pentameric proteins in 50 models. The issues are 1. There are no salt bridges found in the same chain. But I find some if I use this command. >pairwise_dist /model0//A/LYS+ARG/NZ+NE+NH*, >/model0//A/ASP+GLU/OD*+OE*, 4, sh

Re: [PyMOL] PyMOL-users Digest, Vol 177, Issue 5

7; to pymol-users-requ...@lists.sourceforge.net You can reach the person managing the list at pymol-users-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than &qu

[PyMOL] counting salt bridge pairs

/429/OD1 to model1/A/ARG/424/NE: 2.589 model1/E/ASP/429/OD2 to model1/A/ARG/424/NE: 3.604 model1/E/GLU/437/OE2 to model1/E/ARG/310/NE: 3.311 model1/E/ASP/446/OD2 to model1/E/LYS/239/NZ: 3.776 Message: 3 Date: Fri, 12 Feb 2021 14:07:13 + From: "

[PyMOL] list_hb.py

Hi, Pymol Users, I used this script to find hydrogen-bond in protein, list_hb.py. list_hb all, all, write_distances_file=hb I find there are some pairs are clearly not hydrogen bonds, e.g. A/VAL`257/O/774A/MET`261/O/8342.87 Also, the angle is not right for certain pair A/HIS`400/NE2/29

[PyMOL] generate non crystallic subunit

Hi, Pymol-users I have a pentameric protein. However, the PDB only contain one subunit with Biomt info provided as the follows. How can I generate the other four subunit and get the whole pentamer in pymol? Thanks! REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, O, B, C REMARK 350 BIOMT1 1 1

Re: [PyMOL] CCP4 maps not aligning to my PDB file

try this. Matrix Copy - PyMOLWiki Matrix Copy - PyMOLWiki Matrix_copy copies the object matrix from one object to another.. This command is often used after a protein structure alignment to bring other relate

[PyMOL] Exporting data from PyMOL into OriginLab

I often process the images from pymol or originLab in GIMP or photoshop. You could set the pixel content of your pymol image, Png - PyMOLWiki. But I guess this is not the "crop" you expect. Best, Charles Png - PyMOLWiki

[PyMOL] r, theta, and phi of a helix

Hi, Pymol Users, How can I extract the orientation of the helix region of a protein? For example, I have a pentameric membrane protein, I would like to know the orientation angle of one helix region relative to the pentameric symmetry axis (Z)? I found there is a script to calculate the angle