Re: [PyMOL] The 'select' command for complex residue selection
The last parentheses is not the ASCII character ")" (code 41), but the unicode character "）" (code U+FF09) and PyMOL can't handle that. https://www.compart.com/en/unicode/U+FF09 Cheers, Thomas > On Jul 9, 2019, at 5:47 AM, Kevin Jude wrote: > > Strange, I get the same error and can't figure out why it doesn't like the > parentheses around the second term, though here are a few formulations that > give the correct result without syntax errors: > > select sele, protein_A and chain A and (resi 29-33 or resi 70-73 or resi > 116-119) or protein_A and chain C and resi 87-95 > select sele, (protein_A and chain C and resi 87-95) or (protein_A and chain > A and (resi 29-33 or resi 70-73 or resi 116-119)) > select sele, protein_A and chain C and resi 87-95 or (protein_A and chain A > and (resi 29-33 or resi 70-73 or resi 116-119)) > select sele, protein_A and chain C and resi 87-95 or (protein_A and chain A > and resi 29-33 or resi 70-73 or resi 116-119) > > -- > Kevin Jude, PhD > Structural Biology Research Specialist, Garcia Lab > Howard Hughes Medical Institute > Stanford University School of Medicine > Beckman B177, 279 Campus Drive, Stanford CA 94305 > Phone: (650) 723-6431 > > On Mon, Jul 8, 2019 at 7:40 PM sunyeping via PyMOL-users > wrote: > Dear all, > > In pymol I loaded two protein: protein_A and protein_B. I want to make a > selection of some incontinuous residues from two chains of protein_A, for > example, residue 30-34, 71-74 and 117-120 from chain A and residue 88-96 from > chain C. How should I write the select command? I tried the following: > >select sele, (protein_A and chain A and (resi 29-33 or resi 70-73 or resi > 116-119)) or (protein_A and chain C and resi 87-95） > > but it returns syntax error. So what is the correct command for this? > > Thank you in advance -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] The 'select' command for complex residue selection
Hi, Ali, Your command format works well. Thank you. -- From:Ali Kusay Sent At:2019 Jul. 9 (Tue.) 11:11 To:孙业平 Cc:pymol-users Subject:Re: [PyMOL] The 'select' command for complex residue selection Hi Sunyeping, I am not sure where your error is coming from (I noticed you also wrote protein_A in second selection as well). I have however rewritten the command in a simpler way, so try this: select sele, (protein_A and c. A and resi 29-33+70-73+116-119) or (protein_B and c. C and resi 87-95) c. A is equivalent to chain A and this residue selection formats avoid the need of annoying “or” statements Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist The University of Sydney School of Pharmacy | Faculty of Medicine and Health 424, Brain and Mind Centre | The University of Sydney | NSW 2050 Email: akus8...@uni.sydney.edu.au From: sunyeping via PyMOL-users Reply-To: sunyeping Date: Tuesday, 9 July 2019 at 12:41 pm To: pymol-users Subject: [PyMOL] The 'select' command for complex residue selection Dear all, In pymol I loaded two protein: protein_A and protein_B. I want to make a selection of some incontinuous residues from two chains of protein_A, for example, residue 30-34, 71-74 and 117-120 from chain A and residue 88-96 from chain C. How should I write the select command? I tried the following: select sele, (protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119)) or (protein_A and chain C and resi 87-95） but it returns syntax error. So what is the correct command for this? Thank you in advance ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] The 'select' command for complex residue selection
Strange, I get the same error and can't figure out why it doesn't like the parentheses around the second term, though here are a few formulations that give the correct result without syntax errors: select sele, protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119) or protein_A and chain C and resi 87-95 select sele, (protein_A and chain C and resi 87-95) or (protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119)) select sele, protein_A and chain C and resi 87-95 or (protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119)) select sele, protein_A and chain C and resi 87-95 or (protein_A and chain A and resi 29-33 or resi 70-73 or resi 116-119) -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431 On Mon, Jul 8, 2019 at 7:40 PM sunyeping via PyMOL-users < pymol-users@lists.sourceforge.net> wrote: > Dear all, > > In pymol I loaded two protein: protein_A and protein_B. I want to make a > selection of some incontinuous residues from two chains of protein_A, for > example, residue 30-34, 71-74 and 117-120 from chain A and residue 88-96 > from chain C. How should I write the select command? I tried the following: > >select sele, (protein_A > and chain A and (resi 29-33 or resi 70-73 or resi 116-119)) or (protein_A > and chain C and resi 87-95） > > but it returns syntax error. So what is the correct command for this? > > Thank you in advance > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] The 'select' command for complex residue selection
Hi Sunyeping, I am not sure where your error is coming from (I noticed you also wrote protein_A in second selection as well). I have however rewritten the command in a simpler way, so try this: select sele, (protein_A and c. A and resi 29-33+70-73+116-119) or (protein_B and c. C and resi 87-95) c. A is equivalent to chain A and this residue selection formats avoid the need of annoying “or” statements Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist The University of Sydney School of Pharmacy | Faculty of Medicine and Health 424, Brain and Mind Centre | The University of Sydney | NSW 2050 Email: akus8...@uni.sydney.edu.au From: sunyeping via PyMOL-users Reply-To: sunyeping Date: Tuesday, 9 July 2019 at 12:41 pm To: pymol-users Subject: [PyMOL] The 'select' command for complex residue selection Dear all, In pymol I loaded two protein: protein_A and protein_B. I want to make a selection of some incontinuous residues from two chains of protein_A, for example, residue 30-34, 71-74 and 117-120 from chain A and residue 88-96 from chain C. How should I write the select command? I tried the following: select sele, (protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119)) or (protein_A and chain C and resi 87-95） but it returns syntax error. So what is the correct command for this? Thank you in advance ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] The 'select' command for complex residue selection
Dear all, In pymol I loaded two protein: protein_A and protein_B. I want to make a selection of some incontinuous residues from two chains of protein_A, for example, residue 30-34, 71-74 and 117-120 from chain A and residue 88-96 from chain C. How should I write the select command? I tried the following: select sele, (protein_A and chain A and (resi 29-33 or resi 70-73 or resi 116-119)) or (protein_A and chain C and resi 87-95） but it returns syntax error. So what is the correct command for this? Thank you in advance___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] How to calculate RMSD among multiple proteins
Dear all, It is easy to evaluate the simularity of two proteins in pymol. We just need to align them and a RMSD will be given in pymol. However, I want to compare the strutural similiarity of multiple proteins. I can align two of them once and by doing alignment many times, I can finally get pair-wise RMSD of these proteins. Is there any simple method to do? Is there a scriipt that can automatically calculate the pair-wise RMSD among many proteins in pymol? Thank you in advance. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to label secondary structures in pymol
Thank you, Jared. -- From:Jared Sampson Sent At:2019 Jul. 8 (Mon.) 12:08 To:pymol-users ; 孙业平 Subject:Re: [PyMOL] How to label secondary structures in pymol Hi sunyeping - Yes, it is possible. You can pick one atom to label in each SS element. See this old thread: https://sourceforge.net/p/pymol/mailman/message/30823352/. You can also adjust the label position/size/style using the various label settings as well. I would normally direct you to the label wiki page, but that appears (at least to me) to be broken at the moment. So here, instead, is a link to a few-years-old archive of that page. Hope that helps. Cheers, Jared On July 7, 2019 at 1:38:15 PM, sunyeping via PyMOL-users (pymol-users@lists.sourceforge.net) wrote: Dear all, Is it possible to label secondary structures directly in pymol? I mean add a text near local structures which tells the types and numbers of their secondary structures, such as "α1", "β1", "α2", "β2", etc.. Thank you in advance. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] PyMOL-users Digest, Vol 158, Issue 6
Dear Yeping You can color the surface independent of the atom color with the command set surface_color, (color), (selection) similarly, you color the cartoon representation dependent of the atom color with the command set cartoon_color, (color), (selection) best regards Annemarie Dr. Annemarie Honegger Dept. of Biochemistry Zürich University Winterthurerstrasse 190 8057 Zürich Switzerland e-mail: honeg...@bioc.uzh.ch phone: +41 44 635 55 62 fax:+41 44 635 57 12 > > - > > > I?m protected online with Avast Free Antivirus. Get it here ? > it?s free forever. > On Sat, Jul 6, 2019 at 2:29 PM sunyeping via PyMOL-users > wrote: > Dear all, > > I color a protein as blue, display it by surface and cartoon simultaneously, > and set the surface transperant so that the cartoon representation inside the > surface can be seen. I display one residue as stick. I want to color the > stick by element, but keep the surface representation as blue. However, I > don't know how to do this. I can color the residue (please see the Gln in > the yellow circle at > https://drive.google.com/open?id=1bviFQGUKgqLdbE-cUNDtzDZSdabc0N4Z), but both > the stick and the surface representations are colored by element. Could > anyone tell me how to color stick representation of this Gln by element but > keep its surface representation as blue? > > Thank you in advance > Yeping ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
