Re: [PyMOL] some questions about label

Hi, http://www.pymolwiki.org/index.php/Label would help. Zhijian Xu On 09/26/2013 10:40 AM, xfc_2013 wrote: Dear everybody, I'm a new user of pymol and have come with some questions about label. The two main progroms are as following: 1. I have labeled residue names of a receptor protein ar

Re: [PyMOL] new PyMOL extension: psico

Dear Thomas, Wonderful work. I will have a try. Cheers, Zhijian Xu Thomas Holder wrote: > Dear PyMOL users, > > I put a new python module on the PyMOLWiki which is a comprehensive > collection of scripts. It's basically my in-house setup of PyMOL > scripts, where all good stuff which I need r

Re: [PyMOL] Question about ray tracing, set_view, surface smoothness

Hi Gudrun, Gudrun Lotze wrote: > Dear all, > > I wish to ray trace my object so it looks nice. I have chosen a mesh as > surface representation. > > I did > viewport 1024, 768 > ray 1024, 768 > > But the mesh is black afterwards and not anymore blue. > Is there a chance to keep the color and hav

Re: [PyMOL] Open Source PyMOL v1.5.0.1

Dear, I compiled PyMOL 1.5.0.1 from SVN revision 3979 on Centos 5 with python 2.7.1. and found "splash screen 1.3.x" too. Best, Zhijian Xu Troels Emtekær Linnet wrote: > Hi. > > I can confirm that you can compile pymol 1.5.0.1 on RHEL 6, with > python 2.6.6 from the RHEL repositories. > http:/

Re: [PyMOL] about super_all.py Plugin installation.

Dear Pavan, align 4-5 structures at a time (with low sequence identity). check cealign: http://www.pymolwiki.org/index.php/Cealign In pymol1.4, you could use 'alignto': PyMOL>help alignto DESCRIPTION NOTE: This feature is experimental and unsuspported. "alignto" aligns all other loaded objects t

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

Dear Masataka, Will you try update python 2.4.3 to python 2.6 or later? Pymol 1.4.1 works well on my centos5.4. In my case, I both have python 2.7.1 and pytnon 2.4 in the system, and use python 2.7.1 to compile pymol. In addition, the gcc version is 4.1.2. Hope it helps, Zhijian Xu grantaka36

Re: [PyMOL] Multiple Structure Superposition

Dear Suda, cealign can be used to do structure based superposition PyMOL> cealign target, mobile However, it's a pair-wise based alignment. You have to align two structures each time. Hope this helps. Zhijian Xu Suda Ravindran wrote: > Hi, > > I would like to know how to do structure based super

Re: [PyMOL] change label position

Dear leila, Check this: http://www.pymolwiki.org/index.php/Label "enter edit_mode and *ctrl-middle-click* to drag labels around". In this way, you can change the position of one of labels while position of others be fixed

Re: [PyMOL] How to avoid the message "ObjectMoleculeGuessValences" in pymol1.4.1?

Dear Thomas, It works now after taking your advice. Thanks very much. Best Regards, Zhijian Xu Thomas Holder wrote: > On 06/16/2011 04:24 PM, zjxu wrote: >> (3) In pymol/trunk/pymol: >> python setup.py install --prefix=/BioSoft/pymol1.4.1_2011-6-16/ >> python setup2.

Re: [PyMOL] How to avoid the message "ObjectMoleculeGuessValences" in pymol1.4.1?

ect molecule to "blather" then you'll see this > message. > > Please try pulling again (ensuring you have commit 3955) and > rebuilding. I also suggest cleaning the last version before > installing. > > Cheers, > > -- Jason > > On Thu, Jun 16, 2011 a

Re: [PyMOL] How to avoid the message "ObjectMoleculeGuessValences" in pymol1.4.1?

* suppress guess valences warning message to Blather (3) In pymol/trunk/pymol: python setup.py install --prefix=/BioSoft/pymol1.4.1_2011-6-16/ python setup2.py install ./pymol However, when I load a pdb, the warning comes again. "pymol -rkqc script.py" complains again. Best Regards, Zhijia

Re: [PyMOL] How to avoid the message "ObjectMoleculeGuessValences" in pymol1.4.1?

ning message for later versions to be released in a > few months' time. If you're using the open-source code, then a > rebuild from source should fix this for you. I just pushed the change > to the open-source project a few moments ago. > > Cheers, > > -- Jason &g

[PyMOL] How to avoid the message "ObjectMoleculeGuessValences" in pymol1.4.1?

Dear everyone, when I run a script in pymol1.4.1 on the command line: pymol -rqkc script.py. Then a lot of messages "ObjectMoleculeGuessValences(1,1): Unreasonable connectivity in heteroatom, unsuccessful in guessing valences." will be printed out on the screen in addition to the script resul

Re: [PyMOL] cropping the missing residues from other PDB file

Dear Joyce, It sounds like a question related to homology modeling. You could try http://salilab.org/modeller/download_installation.html or http://swissmodel.expasy.org/. In pymol, this may be a rough way: (1) align B to A, (2) create A_complete, A or ( the missing residues from B), (3) Now you

Re: [PyMOL] [Fwd: Re: select residues from different chains]

Dear Maia, Would you like to try this: select bridge, (c. a and i. 160+356+505+507+508) or (c. c and i. 275+355+128) Best Regards, Zhijian Xu Maia Cherney wrote: > Hi Jason, > > I keep sending my e-mail from a wrong address that the pymol mailing > list does nor recognize. > > I need a command

Re: [PyMOL] Pymol problem under Centos 5.4

Dear Harry, In my case, Pymol 1.3 and 1.4.1 work on Centos 5.4 with a GeForce 8400 card (driver: NVIDIA-Linux-x86_64-270.41.19). Zhijian Xu Harry Greenblatt wrote: > BS"D > > Dear All, > >We have a quad core Intel machine with a GeForce 7300 card on which > we recently installed Centos 5.4.

Re: [PyMOL] how to write out a pdb file including all residues 10 A around a ligand or residue?

n density map only for selected > residues, in Coot or pymol or other easy-to-use program :-) ? sorry, did not deal with this task before, maybe the list can help. > > > Sorry for these many questions, and thank you very much for your time!! > > Kindly, > > Jie > > zj

Re: [PyMOL] how to write out a pdb file including all residues 10 A around a ligand or residue?

Dear jie yang, you can use some routine like this: In your pymol: fetch 1ATP create ligand_10A, byres(1ATP within 10 of i. 355) then you can save the object 'ligand_10A' as a pdb file from the menu: file - save molecule i. 355 is the ligand residue ID Or if you do not want the ligand to be includ

Re: [PyMOL] how to print out the atom type in a pymol script

Dear Thomas, at.hetatm works perfectly! Thanks very much. Best Regards, Zhijian Xu Thomas Holder wrote: > Hi Zhijian, > > it's the at.hetatm attribute. > > try this: > print atoms.atom[0].__dict__ > > Cheers, > Thomas > > On Sat, 2010-09-25 at 22:56 +0

[PyMOL] how to print out the atom type in a pymol script

Dear everyone, I could print the atom properties in a script except the atom type: atoms = cmd.get_model("object") for at in atoms.atom: sele1 = model + " and i. " + resi sele2="object and resi %s and name %s"% (at.resi, at.name) #print sele1, sele2 dst=cmd.distance("tmp", s